Index

Symbols

--all-pos seismic-wf command line option --ambindel seismic-relate command line option seismic-wf command line option --barcode-end seismic-demult command line option seismic-wf command line option --barcode-start seismic-demult command line option seismic-wf command line option --batch-size seismic-+sim-relate command line option seismic-relate command line option seismic-wf command line option --brotli-level seismic-+addclust command line option seismic-+delclust command line option seismic-+sim-relate command line option seismic-cluster command line option seismic-mask command line option seismic-relate command line option seismic-wf command line option --bt2-contain seismic-align command line option seismic-wf command line option --bt2-D seismic-align command line option seismic-wf command line option --bt2-discordant seismic-align command line option seismic-wf command line option --bt2-dovetail seismic-align command line option seismic-wf command line option --bt2-dpad seismic-align command line option seismic-wf command line option --bt2-end-to-end seismic-align command line option seismic-wf command line option --bt2-gbar seismic-align command line option seismic-wf command line option --bt2-I seismic-align command line option seismic-wf command line option --bt2-i seismic-align command line option seismic-wf command line option --bt2-L seismic-align command line option seismic-wf command line option --bt2-local seismic-align command line option seismic-wf command line option --bt2-mixed seismic-align command line option seismic-wf command line option --bt2-no-contain seismic-align command line option seismic-wf command line option --bt2-no-discordant seismic-align command line option seismic-wf command line option --bt2-no-dovetail seismic-align command line option seismic-wf command line option --bt2-no-mixed seismic-align command line option seismic-wf command line option --bt2-no-un seismic-align command line option seismic-wf command line option --bt2-orient seismic-align command line option seismic-wf command line option --bt2-R seismic-align command line option seismic-wf command line option --bt2-score-min-e2e seismic-align command line option seismic-wf command line option --bt2-score-min-loc seismic-align command line option seismic-wf command line option --bt2-un seismic-align command line option seismic-wf command line option --bt2-X seismic-align command line option seismic-wf command line option --cgroup seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-wf command line option --clip-end3 seismic-relate command line option seismic-wf command line option --clip-end5 seismic-relate command line option seismic-wf command line option --clipped seismic-demult command line option seismic-wf command line option --clust-conc seismic-+sim-clusts command line option seismic-+sim-params command line option seismic-+sim-total command line option --complement seismic-+listpos command line option --comppair seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-scatter command line option --compself seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-scatter command line option --csv seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-wf command line option --ct-file seismic-+sim-clusts command line option seismic-+sim-ends command line option seismic-+sim-muts command line option seismic-+sim-params command line option --ct-pos-5 seismic-+renumct command line option --cut seismic-align command line option seismic-wf command line option --cut-a1 seismic-align command line option seismic-wf command line option --cut-a2 seismic-align command line option seismic-wf command line option --cut-discard-trimmed seismic-align command line option seismic-wf command line option --cut-discard-untrimmed seismic-align command line option seismic-wf command line option --cut-e seismic-align command line option seismic-wf command line option --cut-g1 seismic-align command line option seismic-wf command line option --cut-g2 seismic-align command line option seismic-wf command line option --cut-indels seismic-align command line option seismic-wf command line option --cut-keep-trimmed seismic-align command line option seismic-wf command line option --cut-keep-untrimmed seismic-align command line option seismic-wf command line option --cut-m seismic-align command line option seismic-wf command line option --cut-nextseq seismic-align command line option seismic-wf command line option --cut-no-indels seismic-align command line option seismic-wf command line option --cut-no-nextseq seismic-align command line option seismic-wf command line option --cut-O seismic-align command line option seismic-wf command line option --cut-q1 seismic-align command line option seismic-wf command line option --cut-q2 seismic-align command line option seismic-wf command line option --demult-off seismic-wf command line option --demult-on seismic-wf command line option --demulti-overwrite seismic-demult command line option seismic-wf command line option --dmfastqx seismic-align command line option seismic-wf command line option --dmfastqy seismic-align command line option seismic-wf command line option --dmfastqz seismic-align command line option seismic-wf command line option --em-runs seismic-cluster command line option seismic-wf command line option --em-thresh seismic-cluster command line option seismic-wf command line option --end3-fmean seismic-+sim-ends command line option seismic-+sim-params command line option seismic-+sim-total command line option --ends-var seismic-+sim-ends command line option seismic-+sim-params command line option seismic-+sim-total command line option --erase-tmp seismic-+sim-fold command line option seismic-+sim-total command line option seismic-align command line option seismic-cluster command line option seismic-demult command line option seismic-fold command line option seismic-mask command line option seismic-relate command line option seismic-wf command line option --exact-unbias seismic-mask command line option seismic-wf command line option --export seismic-wf command line option --f1r2-minus seismic-align command line option seismic-wf command line option --f1r2-plus seismic-align command line option seismic-wf command line option --fastqc seismic-align command line option seismic-wf command line option --fastqx seismic-align command line option seismic-demult command line option seismic-wf command line option --fastqy seismic-align command line option seismic-wf command line option --fastqz seismic-align command line option seismic-wf command line option --fold seismic-wf command line option --fold-constraint seismic-+sim-fold command line option seismic-+sim-total command line option seismic-fold command line option seismic-wf command line option --fold-coords seismic-+sim-fold command line option seismic-+sim-total command line option seismic-fold command line option seismic-graph-aucroll command line option seismic-graph-roc command line option seismic-wf command line option --fold-full seismic-fold command line option seismic-graph-aucroll command line option seismic-graph-roc command line option seismic-wf command line option --fold-max seismic-+sim-fold command line option seismic-+sim-total command line option seismic-fold command line option seismic-wf command line option --fold-md seismic-+sim-fold command line option seismic-+sim-total command line option seismic-fold command line option seismic-wf command line option --fold-mfe seismic-+sim-fold command line option seismic-+sim-total command line option seismic-fold command line option seismic-wf command line option --fold-percent seismic-+sim-fold command line option seismic-+sim-total command line option seismic-fold command line option seismic-wf command line option --fold-primers seismic-+sim-fold command line option seismic-+sim-total command line option seismic-fold command line option seismic-graph-aucroll command line option seismic-graph-roc command line option seismic-wf command line option --fold-sections-file seismic-+sim-fold command line option seismic-+sim-total command line option seismic-fold command line option seismic-graph-aucroll command line option seismic-graph-roc command line option seismic-wf command line option --fold-sub seismic-+sim-fold command line option seismic-+sim-total command line option seismic-fold command line option seismic-wf command line option --fold-table seismic-fold command line option seismic-graph-aucroll command line option seismic-graph-roc command line option seismic-wf command line option --fold-temp seismic-+sim-fold command line option seismic-+sim-total command line option seismic-fold command line option seismic-wf command line option --force seismic-+cleanfa command line option seismic-+listpos command line option seismic-+renumct command line option seismic-+sim-clusts command line option seismic-+sim-ends command line option seismic-+sim-fastq command line option seismic-+sim-fold command line option seismic-+sim-muts command line option seismic-+sim-params command line option seismic-+sim-ref command line option seismic-+sim-relate command line option seismic-+sim-total command line option seismic-align command line option seismic-cluster command line option seismic-fold command line option seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-mask command line option seismic-relate command line option seismic-table command line option seismic-wf command line option --fq-gzip seismic-+sim-fastq command line option seismic-+sim-total command line option --fq-text seismic-+sim-fastq command line option seismic-+sim-total command line option --graph-aucroll seismic-wf command line option --graph-giniroll seismic-wf command line option --graph-mhist seismic-wf command line option --graph-mprof seismic-wf command line option --graph-ncov seismic-wf command line option --graph-roc seismic-wf command line option --graph-tmprof seismic-wf command line option --hist-bins seismic-graph-histpos command line option seismic-graph-histread command line option seismic-wf command line option --hist-margin seismic-graph-histpos command line option seismic-graph-histread command line option seismic-wf command line option --html seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-wf command line option --index-tolerance seismic-demult command line option seismic-wf command line option --inplace seismic-+cleanfa command line option seismic-+renumct command line option --insert-fmean seismic-+sim-ends command line option seismic-+sim-params command line option seismic-+sim-total command line option --join-clusts seismic-wf command line option --joined seismic-wf command line option --keep-del seismic-mask command line option seismic-wf command line option --keep-discontig seismic-mask command line option seismic-wf command line option --keep-gu seismic-mask command line option seismic-wf command line option --keep-ins seismic-mask command line option seismic-wf command line option --keep-tmp seismic-+sim-fold command line option seismic-+sim-total command line option seismic-align command line option seismic-cluster command line option seismic-demult command line option seismic-fold command line option seismic-mask command line option seismic-relate command line option seismic-wf command line option --mask-coords seismic-mask command line option seismic-wf command line option --mask-del seismic-mask command line option seismic-wf command line option --mask-discontig seismic-mask command line option seismic-wf command line option --mask-gu seismic-mask command line option seismic-wf command line option --mask-ins seismic-mask command line option seismic-wf command line option --mask-mut seismic-mask command line option seismic-wf command line option --mask-polya seismic-mask command line option seismic-wf command line option --mask-pos seismic-mask command line option seismic-wf command line option --mask-pos-file seismic-mask command line option seismic-wf command line option --mask-primers seismic-mask command line option seismic-wf command line option --mask-sections-file seismic-mask command line option seismic-wf command line option --max-clusters seismic-+addclust command line option seismic-+delclust command line option seismic-cluster command line option seismic-wf command line option --max-em-iter seismic-cluster command line option seismic-wf command line option --max-fmut-pos seismic-+listpos command line option seismic-mask command line option seismic-wf command line option --max-fmut-read seismic-mask command line option seismic-wf command line option --max-procs seismic-+addclust command line option seismic-+cleanfa command line option seismic-+delclust command line option seismic-+listpos command line option seismic-+renumct command line option seismic-+sim-clusts command line option seismic-+sim-ends command line option seismic-+sim-fastq command line option seismic-+sim-fold command line option seismic-+sim-muts command line option seismic-+sim-params command line option seismic-+sim-relate command line option seismic-+sim-total command line option seismic-align command line option seismic-cluster command line option seismic-fold command line option seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-mask command line option seismic-relate command line option seismic-table command line option seismic-wf command line option --metric seismic-graph-corroll command line option --min-em-iter seismic-cluster command line option seismic-wf command line option --min-finfo-read seismic-mask command line option seismic-wf command line option --min-mapq seismic-align command line option seismic-relate command line option seismic-wf command line option --min-mut-gap seismic-+sim-fastq command line option seismic-+sim-relate command line option seismic-+sim-total command line option seismic-mask command line option seismic-wf command line option --min-ncov-read seismic-mask command line option seismic-wf command line option --min-ninfo-pos seismic-mask command line option seismic-wf command line option --min-phred seismic-relate command line option seismic-wf command line option --min-reads seismic-align command line option seismic-relate command line option seismic-wf command line option --minus-label seismic-align command line option seismic-wf command line option --mismatch-tolerence seismic-demult command line option seismic-wf command line option --mix-strands seismic-align command line option seismic-wf command line option --newfile seismic-+cleanfa command line option seismic-+renumct command line option --no-ambindel seismic-relate command line option seismic-wf command line option --no-complement seismic-+listpos command line option --no-comppair seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-scatter command line option

--no-compself seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-scatter command line option --no-csv seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-wf command line option --no-cut seismic-align command line option seismic-wf command line option --no-export seismic-wf command line option --no-fastqc seismic-align command line option seismic-wf command line option --no-fold seismic-wf command line option --no-force seismic-+cleanfa command line option seismic-+listpos command line option seismic-+renumct command line option seismic-+sim-clusts command line option seismic-+sim-ends command line option seismic-+sim-fastq command line option seismic-+sim-fold command line option seismic-+sim-muts command line option seismic-+sim-params command line option seismic-+sim-ref command line option seismic-+sim-relate command line option seismic-+sim-total command line option seismic-align command line option seismic-cluster command line option seismic-fold command line option seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-mask command line option seismic-relate command line option seismic-table command line option seismic-wf command line option --no-graph-aucroll seismic-wf command line option --no-graph-giniroll seismic-wf command line option --no-graph-mhist seismic-wf command line option --no-graph-mprof seismic-wf command line option --no-graph-ncov seismic-wf command line option --no-graph-roc seismic-wf command line option --no-graph-tmprof seismic-wf command line option --no-html seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-wf command line option --no-overhangs seismic-relate command line option seismic-wf command line option --no-pdf seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-wf command line option --no-png seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-wf command line option --no-svg seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-wf command line option --no-table-clust seismic-table command line option seismic-wf command line option --no-table-pos seismic-table command line option seismic-wf command line option --no-table-read seismic-table command line option seismic-wf command line option --num-reads seismic-+sim-fastq command line option seismic-+sim-relate command line option seismic-+sim-total command line option --out-dir seismic-+cleanfa command line option seismic-+renumct command line option seismic-align command line option seismic-demult command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-scatter command line option seismic-relate command line option seismic-wf command line option --overhangs seismic-relate command line option seismic-wf command line option --paired-end seismic-+sim-fastq command line option seismic-+sim-relate command line option seismic-+sim-total command line option --parallel seismic-+addclust command line option seismic-+cleanfa command line option seismic-+delclust command line option seismic-+listpos command line option seismic-+renumct command line option seismic-+sim-clusts command line option seismic-+sim-ends command line option seismic-+sim-fastq command line option seismic-+sim-fold command line option seismic-+sim-muts command line option seismic-+sim-params command line option seismic-+sim-relate command line option seismic-+sim-total command line option seismic-align command line option seismic-cluster command line option seismic-fold command line option seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-mask command line option seismic-relate command line option seismic-table command line option seismic-wf command line option --parallel-demultiplexing seismic-demult command line option seismic-wf command line option --param-dir seismic-+sim-fastq command line option seismic-+sim-relate command line option --pdf seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-wf command line option --phred-enc seismic-align command line option seismic-demult command line option seismic-relate command line option seismic-wf command line option --pmut-paired seismic-+sim-muts command line option seismic-+sim-params command line option seismic-+sim-total command line option --pmut-unpaired seismic-+sim-muts command line option seismic-+sim-params command line option seismic-+sim-total command line option --png seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-wf command line option --pool seismic-wf command line option --primer-gap seismic-mask command line option seismic-wf command line option --profile-name seismic-+sim-fastq command line option seismic-+sim-fold command line option seismic-+sim-relate command line option seismic-+sim-total command line option --qc-extract seismic-align command line option seismic-wf command line option --qc-no-extract seismic-align command line option seismic-wf command line option --quantile seismic-fold command line option seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-wf command line option --quick-unbias seismic-mask command line option seismic-wf command line option --quick-unbias-thresh seismic-mask command line option seismic-wf command line option --read-length seismic-+sim-fastq command line option seismic-+sim-relate command line option seismic-+sim-total command line option --ref seismic-+sim-ref command line option seismic-+sim-total command line option --reflen seismic-+sim-ref command line option seismic-+sim-total command line option --refs seismic-+sim-ref command line option seismic-+sim-total command line option --refs-meta seismic-demult command line option seismic-wf command line option --rels seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option --reverse-fraction seismic-+sim-fastq command line option seismic-+sim-relate command line option seismic-+sim-total command line option --sample seismic-+sim-fastq command line option seismic-+sim-relate command line option seismic-+sim-total command line option --samples-meta seismic-wf command line option --sep-strands seismic-align command line option seismic-wf command line option --serial seismic-+addclust command line option seismic-+cleanfa command line option seismic-+delclust command line option seismic-+listpos command line option seismic-+renumct command line option seismic-+sim-clusts command line option seismic-+sim-ends command line option seismic-+sim-fastq command line option seismic-+sim-fold command line option seismic-+sim-muts command line option seismic-+sim-params command line option seismic-+sim-relate command line option seismic-+sim-total command line option seismic-align command line option seismic-cluster command line option seismic-fold command line option seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-mask command line option seismic-relate command line option seismic-table command line option seismic-wf command line option --sim-dir seismic-+sim-fold command line option seismic-+sim-ref command line option seismic-+sim-total command line option --single-end seismic-+sim-fastq command line option seismic-+sim-relate command line option seismic-+sim-total command line option --struct-file seismic-graph-aucroll command line option seismic-graph-roc command line option seismic-wf command line option --svg seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-wf command line option --table-clust seismic-table command line option seismic-wf command line option --table-pos seismic-table command line option seismic-wf command line option --table-read seismic-table command line option seismic-wf command line option --tmp-pfx seismic-+addclust command line option seismic-+delclust command line option seismic-+sim-fold command line option seismic-+sim-total command line option seismic-align command line option seismic-cluster command line option seismic-demult command line option seismic-fold command line option seismic-mask command line option seismic-relate command line option seismic-wf command line option --unmasked-pos seismic-wf command line option --use-count seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option --use-ratio seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option --verbose seismic-+test command line option --vmut-paired seismic-+sim-muts command line option seismic-+sim-params command line option seismic-+sim-total command line option --vmut-unpaired seismic-+sim-muts command line option seismic-+sim-params command line option seismic-+sim-total command line option --window seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-wf command line option --winmin seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-wf command line option -3 seismic-+sim-ends command line option seismic-+sim-params command line option seismic-+sim-total command line option seismic-relate command line option seismic-wf command line option -5 seismic-relate command line option seismic-wf command line option -c seismic-+renumct command line option seismic-+sim-clusts command line option seismic-+sim-params command line option seismic-+sim-total command line option seismic-mask command line option seismic-wf command line option -d seismic-+sim-fastq command line option seismic-+sim-relate command line option -e seismic-+sim-ends command line option seismic-+sim-params command line option seismic-+sim-total command line option seismic-cluster command line option seismic-wf command line option -f seismic-+sim-fold command line option seismic-+sim-total command line option seismic-fold command line option seismic-graph-aucroll command line option seismic-graph-roc command line option seismic-wf command line option -i seismic-+sim-clusts command line option seismic-+sim-ends command line option seismic-+sim-muts command line option seismic-+sim-params command line option -J seismic-wf command line option -j seismic-wf command line option -k seismic-+addclust command line option seismic-+delclust command line option seismic-cluster command line option seismic-wf command line option -l seismic-+sim-ends command line option seismic-+sim-params command line option seismic-+sim-total command line option -m seismic-graph-corroll command line option -N seismic-+sim-ref command line option seismic-+sim-total command line option seismic-align command line option seismic-relate command line option seismic-wf command line option -n seismic-+sim-fastq command line option seismic-+sim-relate command line option seismic-+sim-total command line option seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-wf command line option -o seismic-+cleanfa command line option seismic-+renumct command line option seismic-+sim-fold command line option seismic-+sim-ref command line option seismic-+sim-total command line option seismic-align command line option seismic-demult command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-scatter command line option seismic-relate command line option seismic-wf command line option -P seismic-+sim-fastq command line option seismic-+sim-fold command line option seismic-+sim-relate command line option seismic-+sim-total command line option seismic-wf command line option -p seismic-+sim-muts command line option seismic-+sim-params command line option seismic-+sim-total command line option seismic-mask command line option seismic-wf command line option -q seismic-fold command line option seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-wf command line option -R seismic-+sim-ref command line option seismic-+sim-total command line option seismic-demult command line option seismic-wf command line option -r seismic-+sim-ref command line option seismic-+sim-total command line option seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option -S seismic-wf command line option -s seismic-+sim-fastq command line option seismic-+sim-relate command line option seismic-+sim-total command line option seismic-mask command line option seismic-wf command line option -t seismic-+addclust command line option seismic-+delclust command line option seismic-+sim-fold command line option seismic-+sim-total command line option seismic-align command line option seismic-cluster command line option seismic-demult command line option seismic-fold command line option seismic-mask command line option seismic-relate command line option seismic-wf command line option -u seismic-+sim-muts command line option seismic-+sim-params command line option seismic-+sim-total command line option -v seismic-+sim-muts command line option seismic-+sim-params command line option seismic-+sim-total command line option seismic-+test command line option -w seismic-+sim-muts command line option seismic-+sim-params command line option seismic-+sim-total command line option seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-wf command line option -X seismic-align command line option seismic-wf command line option -x seismic-align command line option seismic-demult command line option seismic-wf command line option -Y seismic-align command line option seismic-wf command line option -y seismic-align command line option seismic-wf command line option -Z seismic-align command line option seismic-wf command line option -z seismic-align command line option seismic-wf command line option

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__getitem__() (seismicrna.core.seq.xna.XNA method) __hash__() (seismicrna.core.seq.xna.XNA method) __mul__() (seismicrna.core.seq.xna.XNA method) __repr__() (seismicrna.core.seq.xna.XNA method) __setattr__() (seismicrna.core.report.Report method) __str__() (seismicrna.relate.aux.cigarop.CigarOp method)

A

a (seismicrna.core.rel.pattern.HalfRelPattern attribute) ABS_TOL (seismicrna.core.mu.tests.unbias_test.TestQuickUnbias attribute) accum_fits() (in module seismicrna.core.batch.accum) accum_per_pos() (in module seismicrna.core.batch.accum) accumulate() (in module seismicrna.core.batch.accum) action (seismicrna.graph.onetable.OneTableGraph property) action1 (seismicrna.graph.twotable.TwoTableGraph property) action2 (seismicrna.graph.twotable.TwoTableGraph property) action_sample1 (seismicrna.graph.twotable.TwoTableGraph property) action_sample2 (seismicrna.graph.twotable.TwoTableGraph property) add() (seismicrna.core.seq.refs.RefSeqs method) add_mask() (seismicrna.core.seq.section.Section method) add_orders() (in module seismicrna.cluster.addclust) adjust_counts() (in module seismicrna.table.calc) align_samples() (in module seismicrna.align.write) AlignRefReport (class in seismicrna.align.report) AlignReport (class in seismicrna.align.report) AlignSampleReport (class in seismicrna.align.report) all_patterns() (in module seismicrna.table.calc) allc() (seismicrna.core.rel.pattern.HalfRelPattern class method) (seismicrna.core.rel.pattern.RelPattern class method) AllReadBatch (class in seismicrna.core.batch.read) alph() (seismicrna.core.seq.xna.DNA class method) (seismicrna.core.seq.xna.RNA class method) (seismicrna.core.seq.xna.XNA class method) ansi_codes (seismicrna.core.logs.ColorFormatter attribute) AnsiCode (class in seismicrna.core.logs) any_nan() (in module seismicrna.core.mu.nan) append_files() (in module seismicrna.demult.demultiplex) apply_mask() (in module seismicrna.mask.batch) args_to_cmd() (in module seismicrna.core.extern.shell) array (seismicrna.core.seq.xna.XNA property)

ArrowDataset (class in seismicrna.core.data) as_fancy() (seismicrna.core.rel.pattern.HalfRelPattern class method) as_list_of_tuples() (in module seismicrna.core.task) as_match() (seismicrna.core.rel.pattern.HalfRelPattern class method) as_plain() (seismicrna.core.rel.pattern.HalfRelPattern class method) as_sam() (in module seismicrna.align.sim) as_tuple_str() (in module seismicrna.sim.total) (in module seismicrna.wf) assert_equal() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsAll method) assert_raise() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) assign_clusterings() (in module seismicrna.cluster.compare) auc (seismicrna.core.rna.state.RNAState property) auto() (in module seismicrna.core.arg.docdef) auto_defaults() (in module seismicrna.core.arg.docdef) auto_docstrs() (in module seismicrna.core.arg.docdef) auto_fields() (seismicrna.align.report.AlignReport class method) (seismicrna.cluster.io.ClusterIO class method) (seismicrna.cluster.report.ClusterReport class method) (seismicrna.core.io.file.FileIO class method) (seismicrna.core.io.seq.RefseqIO class method) (seismicrna.fold.report.FoldReport class method) (seismicrna.joinbase.report.JoinClusterReport class method) (seismicrna.joinbase.report.JoinMaskReport class method) (seismicrna.mask.io.MaskIO class method) (seismicrna.mask.report.MaskReport class method) (seismicrna.pool.report.PoolReport class method) (seismicrna.relate.io.RelateIO class method) auto_reframe() (in module seismicrna.core.mu.frame) auto_remove_nan() (in module seismicrna.core.mu.nan) auto_removes_nan() (in module seismicrna.core.mu.nan) AvgTable (class in seismicrna.table.base) AvgTabulator (class in seismicrna.table.calc)

B

batch_nums (seismicrna.core.data.Dataset property) batch_read_index (seismicrna.core.batch.read.ReadBatch property) batch_types() (seismicrna.core.report.BatchedReport class method) BatchedRefseqReport (class in seismicrna.core.report) BatchedReport (class in seismicrna.core.report) bic (seismicrna.cluster.compare.RunOrderResults property) (seismicrna.cluster.em.EmClustering property) BLUE (seismicrna.core.logs.AnsiCode attribute) BOLD (seismicrna.core.logs.AnsiCode attribute) bowtie2_build_cmd() (in module seismicrna.align.xamops) bowtie2_cmd() (in module seismicrna.align.xamops) BOWTIE2_FLAGS (seismicrna.align.fqunit.FastqUnit attribute) bowtie2_inputs (seismicrna.align.fqunit.FastqUnit property) BrickleIO (class in seismicrna.core.io.file)

broadcast_regex() (in module seismicrna.core.mu.tests.frame_test) broadcastable() (in module seismicrna.core.mu.tests.frame_test) btype() (seismicrna.core.io.batch.ReadBatchIO class method) build() (in module seismicrna.core.path) (seismicrna.core.path.Field method) (seismicrna.core.path.Path method) (seismicrna.core.path.Segment method) build_path() (seismicrna.core.io.file.FileIO class method) builddir() (in module seismicrna.core.path) buildpar() (in module seismicrna.core.path) by_read() (seismicrna.table.base.FreqTable class method) (seismicrna.table.base.PosTable class method) (seismicrna.table.base.ReadTable class method) (seismicrna.table.base.Table class method)

C

c (seismicrna.core.rel.pattern.HalfRelPattern attribute) calc_beta_mv() (in module seismicrna.core.stats) calc_beta_params() (in module seismicrna.core.stats) calc_coeff_determ() (in module seismicrna.core.mu.compare) calc_count_per_pos() (in module seismicrna.core.batch.count) calc_count_per_read() (in module seismicrna.core.batch.count) calc_coverage() (in module seismicrna.core.batch.count) calc_dirichlet_mv() (in module seismicrna.core.stats) calc_dirichlet_params() (in module seismicrna.core.stats) calc_dt_minutes() (in module seismicrna.core.report) calc_extra_threads() (in module seismicrna.core.ngs.xam) calc_gini() (in module seismicrna.core.mu.measure) calc_inverse() (in module seismicrna.core.array) calc_mean_pearson() (in module seismicrna.cluster.compare) calc_muts_matrix() (in module seismicrna.core.batch.muts) calc_nrmsd() (in module seismicrna.core.mu.compare) calc_nrmsd_groups() (in module seismicrna.cluster.compare) calc_p_clust() (in module seismicrna.core.mu.unbias) calc_p_clust_given_noclose() (in module seismicrna.core.mu.unbias) calc_p_ends_given_noclose() (in module seismicrna.core.mu.unbias) calc_p_ends_observed() (in module seismicrna.core.mu.unbias) calc_p_noclose() (in module seismicrna.core.mu.unbias) calc_p_noclose_given_ends() (in module seismicrna.core.mu.unbias) calc_params() (in module seismicrna.core.mu.unbias) calc_params_observed() (in module seismicrna.core.mu.unbias) calc_pearson() (in module seismicrna.core.mu.compare) calc_pearson_groups() (in module seismicrna.cluster.compare) calc_quantile() (in module seismicrna.core.mu.scale) calc_ranks() (in module seismicrna.core.mu.scale) calc_reads_per_pos() (in module seismicrna.core.batch.count) calc_rectangluar_sum() (in module seismicrna.core.mu.unbias) calc_rels_per_pos() (in module seismicrna.core.batch.count) calc_rels_per_read() (in module seismicrna.core.batch.count) calc_rms() (in module seismicrna.core.mu.scale) calc_rms_nrmsd() (in module seismicrna.cluster.compare) calc_rmsd() (in module seismicrna.core.mu.compare) calc_rmsd_groups() (in module seismicrna.cluster.compare) calc_signal_noise() (in module seismicrna.core.mu.measure) calc_spanning_sum_slow() (seismicrna.core.mu.tests.unbias_test.TestCalcRectangularSum static method) calc_spearman() (in module seismicrna.core.mu.compare) calc_taken() (in module seismicrna.core.report) calc_true() (seismicrna.core.mu.tests.compare_test.TestCalcCoeffDeterm class method) (seismicrna.core.mu.tests.compare_test.TestCalcPearson class method) (seismicrna.core.mu.tests.compare_test.TestCalcSpearman class method) cast_path() (in module seismicrna.core.path) cgroup_table() (in module seismicrna.graph.base) check_all_done() (in module seismicrna.demult.demultiplex) check_batch_type() (seismicrna.joinbase.data.JoinMutsDataset class method) check_data_path() (in module seismicrna.fold.rnastructure) check_done() (in module seismicrna.demult.demultiplex) check_exists() (seismicrna.demult.demultiplex.super_fastq method) check_fqs_xams() (in module seismicrna.align.write) check_naturals() (in module seismicrna.core.array) check_set() (seismicrna.demult.demultiplex.super_fastq method) CHECKSUM_KEY (seismicrna.mask.write.Masker attribute) ci_count() (seismicrna.table.base.PosTable method) ci_ratio() (seismicrna.table.base.PosTable method) cigar (seismicrna.relate.py.relate.SamRead attribute) CigarOp (class in seismicrna.relate.aux.cigarop) clean_fasta() (in module seismicrna.cleanfa.cleanfa) clust_header (seismicrna.table.calc.ClustTabulator property) cluster() (in module seismicrna.cluster.write) ClusterBatchIO (class in seismicrna.cluster.io) ClusterDataset (class in seismicrna.cluster.data) clustered() (seismicrna.core.header.ClustHeader class method) (seismicrna.core.header.Header class method) (seismicrna.core.header.RelHeader class method) ClusterIO (class in seismicrna.cluster.io) ClusterMutsBatch (class in seismicrna.cluster.batch) ClusterMutsDataset (class in seismicrna.cluster.data) ClusterReadBatch (class in seismicrna.cluster.batch) ClusterReadDataset (class in seismicrna.cluster.data) ClusterReport (class in seismicrna.cluster.report) clusters (seismicrna.cluster.em.EmClustering property) ClustFreqTable (class in seismicrna.table.base) ClustFreqTableLoader (class in seismicrna.table.load)

ClustFreqTableWriter (class in seismicrna.table.write) ClustHeader (class in seismicrna.core.header) ClustPosTable (class in seismicrna.table.base) ClustPosTableLoader (class in seismicrna.table.load) ClustPosTableWriter (class in seismicrna.table.write) ClustReadTable (class in seismicrna.table.base) ClustReadTableLoader (class in seismicrna.table.load) ClustReadTableWriter (class in seismicrna.table.write) clusts (seismicrna.cluster.data.JoinClusterMutsDataset property) (seismicrna.core.header.Header property) ClustTable (class in seismicrna.table.base) ClustTabulator (class in seismicrna.table.calc) cmap (seismicrna.graph.color.ColorMapGraph property) cmds_to_pipe() (in module seismicrna.core.extern.shell) cmds_to_series() (in module seismicrna.core.extern.shell) cmds_to_subshell() (in module seismicrna.core.extern.shell) CODES (seismicrna.core.logs.AnsiCode attribute) codes (seismicrna.core.rel.pattern.HalfRelPattern property) codestring (seismicrna.graph.base.GraphBase property) (seismicrna.graph.rel.MultiRelsGraph property) (seismicrna.graph.rel.OneRelGraph property) col_index (seismicrna.graph.base.GraphBase property) (seismicrna.graph.onetable.OneTableGraph property) (seismicrna.graph.twotable.TwoTableGraph property) col_titles (seismicrna.graph.base.GraphBase property) collate_xam_cmd() (in module seismicrna.core.ngs.xam) ColorFormatter (class in seismicrna.core.logs) ColorMap (class in seismicrna.graph.color) ColorMapGraph (class in seismicrna.graph.color) columns (seismicrna.table.write.TableWriter property) combine_metadata() (in module seismicrna.export.meta) compare() (seismicrna.cluster.tests.em_test.TestExpectation method) (seismicrna.core.mu.tests.unbias_test.TestTriuLog method) (seismicrna.core.mu.tests.unbias_test.TestTriuNorm method) (seismicrna.core.seq.tests.section_test.TestGetWindows method) compare_windows() (in module seismicrna.core.mu.compare) compile() (seismicrna.core.rel.pattern.HalfRelPattern class method) compress() (seismicrna.core.seq.xna.XNA method) CompressedSeq (class in seismicrna.core.seq.xna) compute_auc() (in module seismicrna.core.rna.roc) compute_auc_roc() (in module seismicrna.core.rna.roc) compute_roc_curve() (in module seismicrna.core.rna.roc) compute_rolling_auc() (in module seismicrna.core.rna.roc) conform_series() (in module seismicrna.export.web) contiguous (seismicrna.core.batch.ends.EndCoords property) coord (seismicrna.core.seq.section.Section property) copy() (seismicrna.core.seq.section.Section method) copy_all_run_tables() (in module seismicrna.cluster.csv) copy_single_run_table() (in module seismicrna.cluster.csv) count (seismicrna.core.seq.section.RefSections property) count_base_types() (in module seismicrna.core.batch.index) count_cigar_muts() (in module seismicrna.relate.aux.cigarop) count_cigar_read() (in module seismicrna.relate.aux.cigarop) count_cigar_ref() (in module seismicrna.relate.aux.cigarop) count_end_coords() (in module seismicrna.core.batch.count) count_fastq_reads() (in module seismicrna.align.fqunit) count_per_pos() (seismicrna.core.batch.muts.SectionMutsBatch method) count_per_read() (seismicrna.core.batch.muts.SectionMutsBatch method) count_pos() (in module seismicrna.core.mu.dim) count_reads_segments() (in module seismicrna.core.batch.ends) count_single_paired() (in module seismicrna.core.ngs.xam) count_total_reads() (in module seismicrna.core.ngs.xam) counts_pos() (in module seismicrna.core.mu.dim) counts_pos_consensus() (in module seismicrna.core.mu.dim) cover_per_pos (seismicrna.core.batch.muts.SectionMutsBatch property) cover_per_read (seismicrna.core.batch.muts.SectionMutsBatch property) create_path_type() (in module seismicrna.core.path) create_report() (in module seismicrna.demult.demultiplex) (seismicrna.mask.write.Masker method) create_tmp_sam() (seismicrna.relate.sam.XamViewer method) ct_data (seismicrna.core.rna.struct.RNAStructure property) ct_text (seismicrna.core.rna.struct.RNAStructure property) ct_title (seismicrna.core.rna.struct.RNAStructure property) ct_to_db() (in module seismicrna.core.rna.io) cutadapt_cmd() (in module seismicrna.align.fqops) cutadapt_input_args (seismicrna.align.fqunit.FastqUnit property) CYAN (seismicrna.core.logs.AnsiCode attribute)

D

data (seismicrna.graph.aucroll.RollingAUCGraph property) (seismicrna.graph.base.GraphBase property) (seismicrna.graph.histrel.RelHistogramGraph property) (seismicrna.graph.profile.ProfileGraph property) (seismicrna.graph.roc.ROCGraph property) (seismicrna.graph.scatter.ScatterPlotGraph property) (seismicrna.graph.statroll.RollingStatGraph property) (seismicrna.graph.twotable.TwoTableMergedGraph property) (seismicrna.table.base.FreqTable property) (seismicrna.table.base.RelTypeTable property) (seismicrna.table.base.Table property) (seismicrna.table.load.ClustFreqTableLoader property) (seismicrna.table.load.RelTypeTableLoader property) (seismicrna.table.write.ClustFreqTableWriter property) (seismicrna.table.write.PosTableWriter property) (seismicrna.table.write.ReadTableWriter property) data1 (seismicrna.graph.twotable.TwoTableGraph property) data2 (seismicrna.graph.twotable.TwoTableGraph property) data_header (seismicrna.graph.histrel.RelHistogramGraph property) (seismicrna.graph.profile.ProfileGraph property) data_kind (seismicrna.graph.base.GraphBase property) Dataset (class in seismicrna.core.data) dataset_types (seismicrna.core.data.LoadFunction property) db_structure (seismicrna.core.rna.struct.RNAStructure property) db_title (seismicrna.core.rna.struct.RNAStructure property) db_to_ct() (in module seismicrna.core.rna.io) decode_phred() (in module seismicrna.core.ngs.phred) decompile() (seismicrna.core.rel.pattern.HalfRelPattern class method) decompress() (in module seismicrna.core.seq.xna) (seismicrna.core.seq.xna.CompressedSeq method) deduplicate() (in module seismicrna.core.path) deduplicated() (in module seismicrna.core.path)

default (seismicrna.core.report.Field attribute) (seismicrna.core.report.OptionField attribute) default_key() (in module seismicrna.core.report) del_orders() (in module seismicrna.cluster.delclust) del_pos3 (seismicrna.relate.py.ambindel.Indel property) del_pos5 (seismicrna.relate.py.ambindel.Indel property) delete_tmp_sam() (seismicrna.relate.sam.XamViewer method) Deletion (class in seismicrna.relate.py.ambindel) delta_log_like (seismicrna.cluster.em.EmClustering property) DeltaProfileGraph (class in seismicrna.graph.delprof) DeltaProfileRunner (class in seismicrna.graph.delprof) DeltaProfileWriter (class in seismicrna.graph.delprof) demultiplex_run() (in module seismicrna.demult.demultiplex) dependency_exists() (in module seismicrna.core.extern.depend) DependencyError destroy_temp_data() (seismicrna.demult.demultiplex.super_fastq method) details (seismicrna.graph.base.GraphBase property) (seismicrna.graph.corroll.RollingCorrelationGraph property) (seismicrna.graph.roll.RollingGraph property) dict (seismicrna.core.rna.struct.RNAStructure property) (seismicrna.core.seq.section.RefSections property) dict_to_pairs() (in module seismicrna.core.rna.pair) dict_to_table() (in module seismicrna.core.rna.pair) digest_data() (in module seismicrna.core.io.brickle) dir_seg_types() (seismicrna.align.report.AlignReport class method) (seismicrna.core.io.file.FileIO class method) (seismicrna.core.io.file.RefIO class method) (seismicrna.core.io.file.SectIO class method) (seismicrna.fold.report.FoldReport class method) dispatch() (in module seismicrna.core.task) DNA (class in seismicrna.core.seq.xna) dtype (seismicrna.core.report.Field attribute) (seismicrna.core.report.OptionField attribute)

E

EmClustering (class in seismicrna.cluster.em) encode_match() (in module seismicrna.relate.py.encode) encode_phred() (in module seismicrna.core.ngs.phred) encode_relate() (in module seismicrna.relate.py.encode) END (seismicrna.core.logs.AnsiCode attribute) end() (seismicrna.core.logs.AnsiCode class method) end3 (seismicrna.core.data.Dataset property) (seismicrna.core.data.LoadedDataset property) (seismicrna.core.data.LoadedMutsDataset property) (seismicrna.core.data.MultistepDataset property) (seismicrna.core.data.TallDataset property) (seismicrna.core.data.WideDataset property) (seismicrna.core.rna.base.RNASection property) (seismicrna.table.base.PosTable property) end3s (seismicrna.cluster.em.EmClustering property) end5 (seismicrna.core.data.Dataset property) (seismicrna.core.data.LoadedDataset property) (seismicrna.core.data.LoadedMutsDataset property) (seismicrna.core.data.MultistepDataset property) (seismicrna.core.data.TallDataset property) (seismicrna.core.data.WideDataset property) (seismicrna.core.rna.base.RNASection property) (seismicrna.table.base.PosTable property)

end5s (seismicrna.cluster.em.EmClustering property) EndCoords (class in seismicrna.core.batch.ends) ensure_order() (in module seismicrna.core.array) ensure_same_length() (in module seismicrna.core.array) exc_info() (in module seismicrna.core.logs) expand_degenerate_seq() (in module seismicrna.core.seq.xna) export_cmd() (in module seismicrna.align.xamops) export_sample() (in module seismicrna.export.web) ext() (seismicrna.table.base.Table class method) ext_type (seismicrna.core.path.Segment property) extract_fasta_seqname() (in module seismicrna.core.seq.fasta) exts (seismicrna.core.path.Segment property)

F

FASTA seismic-+sim-fold command line option seismic-align command line option seismic-demult command line option seismic-relate command line option seismic-wf command line option FastaCleaner (class in seismicrna.cleanfa.cleanfa) fastq_gz() (in module seismicrna.align.fqunit) fastq_to_dict() (seismicrna.demult.demultiplex.super_fastq method) fastqc_cmd() (in module seismicrna.align.fqops) FastqUnit (class in seismicrna.align.fqunit) fetch_count() (seismicrna.table.base.RelTypeTable method) fetch_ratio() (seismicrna.table.base.RelTypeTable method) Field (class in seismicrna.core.path) (class in seismicrna.core.report) field_keys() (in module seismicrna.core.report) (seismicrna.core.report.Report class method) field_titles() (in module seismicrna.core.report) fields() (in module seismicrna.core.report) (seismicrna.align.fqunit.FastqUnit method) (seismicrna.align.report.AlignRefReport class method) (seismicrna.align.report.AlignReport class method) (seismicrna.align.report.AlignSampleReport class method) (seismicrna.cluster.report.ClusterReport class method) (seismicrna.core.report.BatchedReport class method) (seismicrna.core.report.RefseqReport class method) (seismicrna.core.report.Report class method) (seismicrna.fold.report.FoldReport class method) (seismicrna.joinbase.report.JoinClusterReport class method) (seismicrna.joinbase.report.JoinMaskReport class method) (seismicrna.mask.report.MaskReport class method) (seismicrna.pool.report.PoolReport class method) (seismicrna.relate.report.RelateReport class method) figure (seismicrna.graph.base.GraphBase property) figure_alignments() (in module seismicrna.align.write) file_seg_type() (seismicrna.align.report.AlignRefReport class method) (seismicrna.align.report.AlignSampleReport class method) (seismicrna.cluster.io.ClusterBatchIO class method) (seismicrna.cluster.report.ClusterReport class method) (seismicrna.core.io.file.FileIO class method) (seismicrna.core.io.seq.RefseqIO class method) (seismicrna.fold.report.FoldReport class method) (seismicrna.joinbase.report.JoinClusterReport class method) (seismicrna.joinbase.report.JoinMaskReport class method) (seismicrna.mask.io.MaskBatchIO class method) (seismicrna.mask.report.MaskReport class method) (seismicrna.pool.report.PoolReport class method) (seismicrna.relate.io.QnamesBatchIO class method) (seismicrna.relate.io.RelateBatchIO class method) (seismicrna.relate.report.RelateReport class method) FileIO (class in seismicrna.core.io.file) fill_whitespace() (in module seismicrna.core.path) filter_cmd() (in module seismicrna.align.xamops) filter_cmds() (in module seismicrna.align.xamops) find_all_tables() (in module seismicrna.table.load) find_ambindels() (in module seismicrna.relate.py.ambindel) find_best_order() (in module seismicrna.cluster.compare) find_cigar_op_pos() (in module seismicrna.relate.aux.cigarop) find_contiguous_reads() (in module seismicrna.core.batch.ends) find_ct_files() (in module seismicrna.fold.load) find_ct_section() (in module seismicrna.core.rna.io) find_dims() (in module seismicrna.core.array) find_enclosing_pairs() (in module seismicrna.core.rna.pair)

find_files() (in module seismicrna.core.path) find_files_chain() (in module seismicrna.core.path) find_foldable_tables() (in module seismicrna.fold.main) find_pos() (in module seismicrna.lists.listpos) find_pos_tables() (in module seismicrna.table.load) find_read_end3s() (in module seismicrna.core.batch.ends) find_read_end5s() (in module seismicrna.core.batch.ends) find_read_tables() (in module seismicrna.table.load) find_rels_line() (in module seismicrna.relate.py.relate) find_root_pairs() (in module seismicrna.core.rna.pair) find_tables() (in module seismicrna.table.load) find_true_dists() (in module seismicrna.core.array) finds_multigrepped_reads() (in module seismicrna.demult.demultiplex) first (seismicrna.relate.py.relate.SamFlag attribute) fit_uint_size() (in module seismicrna.core.types) fit_uint_type() (in module seismicrna.core.types) fits() (seismicrna.core.rel.pattern.HalfRelPattern method) (seismicrna.core.rel.pattern.RelPattern method) flag (seismicrna.relate.py.relate.SamFlag attribute) (seismicrna.relate.py.relate.SamRead attribute) flagstat_cmd() (in module seismicrna.core.ngs.xam) flagstats (seismicrna.relate.sam.XamViewer property) fmt() (seismicrna.core.logs.AnsiCode class method) fmt_fancy (seismicrna.core.rel.pattern.HalfRelPattern attribute) fmt_func_args() (in module seismicrna.core.task) fmt_plain (seismicrna.core.rel.pattern.HalfRelPattern attribute) fold() (in module seismicrna.fold.rnastructure) fold_profile() (in module seismicrna.fold.main) fold_section() (in module seismicrna.fold.main) (in module seismicrna.sim.fold) FoldReport (class in seismicrna.fold.report) format() (seismicrna.core.logs.ColorFormatter method) format_clust_name() (in module seismicrna.core.header) format_clust_names() (in module seismicrna.core.header) format_db_structure() (in module seismicrna.core.rna.db) format_exp_count_col() (in module seismicrna.cluster.compare) format_fasta_name_line() (in module seismicrna.core.seq.fasta) format_fasta_record() (in module seismicrna.core.seq.fasta) format_fasta_seq_lines() (in module seismicrna.core.seq.fasta) format_metadata() (in module seismicrna.export.web) format_read_name() (in module seismicrna.relate.batch) format_retitled_ct_line() (in module seismicrna.fold.rnastructure) format_version() (in module seismicrna.core.version) four() (seismicrna.core.seq.xna.XNA class method) fpr (seismicrna.graph.roc.ROCGraph property) fq_pipeline() (in module seismicrna.align.write) fqs_pipeline() (in module seismicrna.align.write) FreqTable (class in seismicrna.table.base) from_clusters() (seismicrna.cluster.report.ClusterReport class method) from_counts() (seismicrna.core.rel.pattern.HalfRelPattern class method) (seismicrna.core.rel.pattern.RelPattern class method) from_ct() (in module seismicrna.core.rna.io) from_dataset() (seismicrna.cluster.uniq.UniqReads class method) from_dataset_contig() (seismicrna.cluster.uniq.UniqReads class method) from_db() (in module seismicrna.core.rna.io) from_dict() (seismicrna.core.report.Report class method) from_param_dir() (in module seismicrna.sim.fastq) (in module seismicrna.sim.relate) from_paths() (seismicrna.align.fqunit.FastqUnit class method) from_reads() (in module seismicrna.relate.io) from_report() (in module seismicrna.sim.fastq) from_report_format() (seismicrna.core.rel.pattern.HalfRelPattern class method) from_struct_profile() (seismicrna.core.rna.state.RNAState class method) FullTabulator (class in seismicrna.table.calc)

G

g (seismicrna.core.rel.pattern.HalfRelPattern attribute) generate_batch() (in module seismicrna.relate.write) generate_fastq() (in module seismicrna.sim.fastq) generate_fastq_record() (in module seismicrna.sim.fastq) get() (seismicrna.core.seq.refs.RefSeqs method) (seismicrna.graph.color.ColorMap method) get_action_name() (in module seismicrna.graph.base) get_alphaset() (seismicrna.core.seq.xna.XNA class method) get_args_count_fastq_reads() (in module seismicrna.align.fqunit) get_batch() (seismicrna.core.data.Dataset method) (seismicrna.core.data.LoadedDataset method) (seismicrna.core.data.MultistepDataset method) (seismicrna.core.data.TallDataset method) (seismicrna.core.data.WideDataset method) (seismicrna.relate.data.RelateDataset method) get_batch_checksum() (seismicrna.core.data.LoadedDataset method) get_batch_path() (seismicrna.core.data.LoadedDataset method) get_batch_type() (seismicrna.cluster.data.ClusterReadDataset class method) (seismicrna.cluster.data.JoinClusterMutsDataset class method) (seismicrna.core.data.LoadedDataset class method) (seismicrna.core.report.BatchedReport class method) (seismicrna.joinbase.data.JoinMutsDataset class method) (seismicrna.mask.data.JoinMaskMutsDataset class method) (seismicrna.mask.data.MaskReadDataset class method) (seismicrna.relate.data.QnamesDataset class method) (seismicrna.relate.data.RelateDataset class method) get_bounds() (seismicrna.graph.hist.HistogramGraph method) get_bowtie2_index_paths() (in module seismicrna.align.xamops) get_btype_name() (seismicrna.core.data.LoadedDataset class method) get_byte_dtype() (in module seismicrna.core.types) get_cmap() (in module seismicrna.graph.color) get_cmap_type() (seismicrna.graph.color.ColorMapGraph class method) (seismicrna.graph.delprof.DeltaProfileGraph class method) (seismicrna.graph.histrel.RelHistogramGraph class method) (seismicrna.graph.profile.MultiRelsProfileGraph class method) (seismicrna.graph.profile.OneRelProfileGraph class method) (seismicrna.graph.scatter.ScatterPlotGraph class method) get_colormaps() (in module seismicrna.graph.color) get_common_best_run_attr() (in module seismicrna.cluster.compare) get_common_order() (in module seismicrna.cluster.compare) get_comp() (seismicrna.core.seq.xna.XNA class method) get_comp_func() (in module seismicrna.core.mu.compare) get_comp_name() (in module seismicrna.core.mu.compare) get_comptrans() (seismicrna.core.seq.xna.XNA class method) get_config() (in module seismicrna.core.logs) get_coords_by_ref() (in module seismicrna.core.seq.section) get_count_path() (in module seismicrna.cluster.csv) get_cov_matrix() (seismicrna.cluster.uniq.UniqReads method) get_ct_file() (seismicrna.core.rna.profile.RNAProfile method) get_ct_path() (in module seismicrna.sim.fold) get_dataset1_load_func() (seismicrna.cluster.data.ClusterMutsDataset class method) (seismicrna.core.data.MultistepDataset class method) (seismicrna.mask.data.MaskMutsDataset class method) get_dataset1_report_file() (seismicrna.core.data.MultistepDataset class method) get_dataset2_load_func() (seismicrna.core.data.MultistepDataset class method) get_dataset2_type() (seismicrna.cluster.data.ClusterMutsDataset class method) (seismicrna.core.data.MultistepDataset class method) (seismicrna.mask.data.MaskMutsDataset class method) get_dataset_load_func() (seismicrna.cluster.data.JoinClusterMutsDataset class method) (seismicrna.core.data.MergedDataset class method) (seismicrna.mask.data.JoinMaskMutsDataset class method) (seismicrna.pool.data.PoolDataset class method) get_db_file() (seismicrna.core.rna.profile.RNAProfile method) get_db_structs() (in module seismicrna.export.web) get_db_text() (seismicrna.core.rna.struct.RNAStructure method) get_dms_file() (seismicrna.core.rna.profile.RNAProfile method) get_docstr_lines() (in module seismicrna.core.arg.docdef) get_dtype() (in module seismicrna.core.types) get_edges() (seismicrna.graph.hist.HistogramGraph method) get_edges_index() (in module seismicrna.graph.hist) get_fasta() (seismicrna.core.rna.profile.RNAProfile method) get_fasta_path() (in module seismicrna.sim.ref) get_fasta_seq() (in module seismicrna.core.seq.fasta) get_field() (seismicrna.core.report.Report method) get_fields_in_seg_types() (in module seismicrna.core.path) get_graph() (seismicrna.graph.aucroll.RollingAUCWriter method) (seismicrna.graph.histrel.RelHistogramWriter method) (seismicrna.graph.onetable.OneTableWriter method) (seismicrna.graph.profile.ProfileWriter method) (seismicrna.graph.roc.ROCWriter method) (seismicrna.graph.statroll.RollingStatWriter method) get_graph_type() (seismicrna.graph.corroll.RollingCorrelationWriter class method) (seismicrna.graph.delprof.DeltaProfileWriter class method) (seismicrna.graph.giniroll.RollingGiniWriter class method) (seismicrna.graph.histpos.PosHistogramWriter class method) (seismicrna.graph.histread.ReadHistogramWriter class method) (seismicrna.graph.histrel.RelHistogramWriter class method) (seismicrna.graph.scatter.ScatterPlotWriter class method) (seismicrna.graph.snrroll.RollingSNRWriter class method) (seismicrna.graph.statroll.RollingStatWriter class method) (seismicrna.graph.twotable.TwoTableWriter class method) get_hist_trace() (in module seismicrna.graph.trace) get_length() (in module seismicrna.core.array) get_line_trace() (in module seismicrna.graph.trace) get_list_path() (in module seismicrna.lists.lists) get_log_exp_obs_counts() (in module seismicrna.cluster.compare) get_mask() (seismicrna.core.seq.section.Section method) get_max_uint() (in module seismicrna.core.types) get_max_value() (in module seismicrna.core.types) get_members() (seismicrna.cluster.em.EmClustering method) get_mus() (seismicrna.cluster.em.EmClustering method) get_mut_matrix() (seismicrna.cluster.uniq.UniqReads method) get_non_seq_regex() (in module seismicrna.cleanfa.cleanfa) get_nonalphaset() (seismicrna.core.seq.xna.XNA class method)

get_null_value() (seismicrna.table.calc.FullTabulator class method) (seismicrna.table.calc.PartialTabulator class method) (seismicrna.table.calc.Tabulator class method) get_num_parallel() (in module seismicrna.core.task) get_oconv_array_float() (in module seismicrna.core.report) get_oconv_dict_float() (in module seismicrna.core.report) get_oconv_dict_list_float() (in module seismicrna.core.report) get_oconv_float() (in module seismicrna.core.report) get_oconv_list_float() (in module seismicrna.core.report) get_other_iupac() (seismicrna.core.seq.xna.XNA class method) get_param_default() (in module seismicrna.core.arg.docdef) get_param_dir_fields() (in module seismicrna.sim.relate) get_param_lines() (in module seismicrna.core.arg.docdef) get_path() (seismicrna.core.io.file.FileIO method) (seismicrna.graph.base.GraphBase method) get_path_fields() (seismicrna.graph.base.GraphBase method) (seismicrna.graph.onestruct.StructOneTableGraph method) get_path_segs() (seismicrna.graph.base.GraphBase class method) get_pictrans() (seismicrna.core.seq.xna.XNA class method) get_props() (seismicrna.cluster.em.EmClustering method) get_ref_metadata() (in module seismicrna.export.web) get_rel_name() (in module seismicrna.table.base) get_release_working_dirs() (in module seismicrna.core.tmp) get_report_type() (seismicrna.cluster.data.ClusterReadDataset class method) (seismicrna.cluster.data.JoinClusterMutsDataset class method) (seismicrna.core.data.Dataset class method) (seismicrna.core.data.LoadedDataset class method) (seismicrna.core.data.MultistepDataset class method) (seismicrna.mask.data.JoinMaskMutsDataset class method) (seismicrna.mask.data.MaskReadDataset class method) (seismicrna.pool.data.PoolDataset class method) (seismicrna.relate.data.QnamesDataset class method) (seismicrna.relate.data.RelateDataset class method) get_roc_trace() (in module seismicrna.graph.trace) get_rolling_auc_trace() (in module seismicrna.graph.trace) get_sample_data() (in module seismicrna.export.web) get_sample_metadata() (in module seismicrna.export.web) get_sample_ref_exts() (seismicrna.align.fqunit.FastqUnit method) get_sect_coords_primers() (in module seismicrna.core.seq.section) get_sect_metadata() (in module seismicrna.export.web) get_seq_base_bar_trace() (in module seismicrna.graph.trace) get_seq_base_scatter_trace() (in module seismicrna.graph.trace) get_seq_line_trace() (in module seismicrna.graph.trace) get_seq_stack_bar_trace() (in module seismicrna.graph.trace) get_shared_index() (in module seismicrna.core.seq.section) get_table_data() (in module seismicrna.export.web) get_table_finder() (seismicrna.graph.base.GraphRunner class method) (seismicrna.graph.base.PosGraphRunner class method) (seismicrna.graph.base.ReadGraphRunner class method) (seismicrna.graph.onestruct.StructOneTableRunner class method) get_table_loader() (seismicrna.graph.base.GraphWriter class method) (seismicrna.graph.base.PosGraphWriter class method) (seismicrna.graph.base.ReadGraphWriter class method) get_table_path() (in module seismicrna.cluster.csv) get_tabulator_writer_types() (in module seismicrna.table.write) get_tabulator_writers() (in module seismicrna.table.write) get_top_logger() (in module seismicrna.core.logs) get_traces() (seismicrna.graph.aucroll.RollingAUCGraph method) (seismicrna.graph.base.GraphBase method) (seismicrna.graph.histrel.RelHistogramGraph method) (seismicrna.graph.profile.MultiRelsProfileGraph method) (seismicrna.graph.profile.OneRelProfileGraph method) (seismicrna.graph.roc.ROCGraph method) (seismicrna.graph.scatter.ScatterPlotGraph method) (seismicrna.graph.statroll.RollingStatGraph method) (seismicrna.graph.twotable.TwoTableMergedGraph method) get_uint_dtype() (in module seismicrna.core.types) get_uint_size() (in module seismicrna.core.types) get_uint_type() (in module seismicrna.core.types) get_uniq_names() (seismicrna.cluster.uniq.UniqReads method) get_uniq_reads() (in module seismicrna.cluster.uniq) get_varna_color_file() (seismicrna.core.rna.profile.RNAProfile method) get_verbosity() (in module seismicrna.core.logs) get_writer_type() (seismicrna.graph.aucroll.RollingAUCRunner class method) (seismicrna.graph.base.GraphRunner class method) (seismicrna.graph.corroll.RollingCorrelationRunner class method) (seismicrna.graph.delprof.DeltaProfileRunner class method) (seismicrna.graph.giniroll.RollingGiniRunner class method) (seismicrna.graph.histpos.PosHistogramRunner class method) (seismicrna.graph.histread.ReadHistogramRunner class method) (seismicrna.graph.profile.ProfileRunner class method) (seismicrna.graph.roc.ROCRunner class method) (seismicrna.graph.scatter.ScatterPlotRunner class method) (seismicrna.graph.snrroll.RollingSNRRunner class method) (seismicrna.graph.twotable.TwoTableRunner class method) graph_filename (seismicrna.graph.base.GraphBase property) graph_kind() (seismicrna.graph.aucroll.RollingAUCGraph class method) (seismicrna.graph.base.GraphBase class method) (seismicrna.graph.corroll.RollingCorrelationGraph class method) (seismicrna.graph.delprof.DeltaProfileGraph class method) (seismicrna.graph.giniroll.RollingGiniGraph class method) (seismicrna.graph.histpos.PosHistogramGraph class method) (seismicrna.graph.histread.ReadHistogramGraph class method) (seismicrna.graph.profile.ProfileGraph class method) (seismicrna.graph.roc.ROCGraph class method) (seismicrna.graph.scatter.ScatterPlotGraph class method) (seismicrna.graph.snrroll.RollingSNRGraph class method) GraphBase (class in seismicrna.graph.base) GraphRunner (class in seismicrna.graph.base) GraphWriter (class in seismicrna.graph.base) GREEN (seismicrna.core.logs.AnsiCode attribute) grep_both_fastq() (in module seismicrna.demult.demultiplex) guess_data_path() (in module seismicrna.fold.rnastructure) gzipped() (seismicrna.table.base.Table class method)

H

HalfRelPattern (class in seismicrna.core.rel.pattern) Header (class in seismicrna.core.header) header (seismicrna.table.base.Table property) header_depth() (seismicrna.table.base.Table class method) header_rows() (seismicrna.table.base.RelTypeTable class method) header_type() (seismicrna.table.base.AvgTable class method) (seismicrna.table.base.ClustFreqTable class method) (seismicrna.table.base.ClustTable class method) (seismicrna.table.base.Table class method)

HistogramGraph (class in seismicrna.graph.hist) HistogramRunner (class in seismicrna.graph.hist) humanize_relvec() (in module seismicrna.relate.aux.human) hyphen (seismicrna.core.seq.section.Section property) hyphenate_ends() (in module seismicrna.core.seq.section)

I

iconv (seismicrna.core.report.Field attribute) (seismicrna.core.report.OptionField attribute) iconv_array_int() (in module seismicrna.core.report) iconv_datetime() (in module seismicrna.core.report) iconv_dict_str_dict_int_dict_int_int() (in module seismicrna.core.report) iconv_dict_str_int() (in module seismicrna.core.report) iconv_int_keys() (in module seismicrna.core.report) idxstats_cmd() (in module seismicrna.core.ngs.xam) Indel (class in seismicrna.relate.py.ambindel) index (seismicrna.core.header.ClustHeader property) (seismicrna.core.header.Header property) (seismicrna.core.header.RelClustHeader property) (seismicrna.core.header.RelHeader property) index_clusts() (in module seismicrna.core.header) index_cols() (seismicrna.table.base.Table class method) index_depth() (seismicrna.table.base.ClustFreqTable class method) (seismicrna.table.base.PosTable class method) (seismicrna.table.base.ReadTable class method) (seismicrna.table.base.Table class method) index_order_clusts() (in module seismicrna.core.header) index_orders() (in module seismicrna.core.header) index_orders_clusts() (in module seismicrna.core.header) index_to_pos() (in module seismicrna.core.seq.section) index_to_seq() (in module seismicrna.core.seq.section) index_xam_cmd() (in module seismicrna.core.ngs.xam) indexes (seismicrna.relate.sam.XamViewer property) infer_read() (in module seismicrna.relate.aux.infer) init_args (seismicrna.core.rna.base.RNASection property) (seismicrna.core.rna.profile.RNAProfile property) (seismicrna.core.rna.struct.RNAStructure property) INPUT_PATH seismic-+addclust command line option seismic-+cleanfa command line option seismic-+delclust command line option seismic-+listpos command line option seismic-+sim-fastq command line option seismic-cluster command line option seismic-fold command line option seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-mask command line option seismic-relate command line option seismic-table command line option seismic-wf command line option

ins_pos (seismicrna.relate.py.ambindel.Indel property) Insertion (class in seismicrna.relate.py.ambindel) intersect() (in module seismicrna.core.seq.section) (seismicrna.core.rel.pattern.HalfRelPattern method) (seismicrna.core.rel.pattern.RelPattern method) iopaths() (in module seismicrna.core.extern.shell) is_dataset_type() (seismicrna.core.data.LoadFunction method) is_paired (seismicrna.core.rna.struct.RNAStructure property) iter() (seismicrna.core.seq.refs.RefSeqs method) iter_alignments() (in module seismicrna.relate.aux.iterread) iter_base_types() (in module seismicrna.core.batch.index) iter_batches() (seismicrna.core.data.Dataset method) iter_cases() (seismicrna.relate.py.tests.relate_test.TestFindRelsLine method) iter_clust_indexes() (seismicrna.core.header.Header method) iter_clust_table_data() (in module seismicrna.export.web) iter_graphs() (seismicrna.graph.base.GraphWriter method) (seismicrna.graph.onestruct.StructOneTableWriter method) (seismicrna.graph.onetable.OneTableWriter method) (seismicrna.graph.twotable.TwoTableWriter method) iter_hist_traces() (in module seismicrna.graph.trace) iter_line_traces() (in module seismicrna.graph.trace) iter_pos_table_data() (in module seismicrna.export.web) iter_pos_table_pairs() (in module seismicrna.graph.twotable) iter_pos_table_series() (in module seismicrna.export.web) iter_pos_table_struct() (in module seismicrna.export.web) iter_profiles() (seismicrna.graph.onestruct.StructOneTableGraph method) (seismicrna.table.base.PosTable method) iter_read_table_data() (in module seismicrna.export.web) iter_read_table_pairs() (in module seismicrna.graph.twotable) iter_reads() (seismicrna.core.batch.muts.SectionMutsBatch method) iter_records() (seismicrna.relate.sam.XamViewer method) iter_relvecs_all() (in module seismicrna.relate.aux.iterrel) iter_relvecs_q53() (in module seismicrna.relate.aux.iterrel) iter_roc_traces() (in module seismicrna.graph.trace) iter_rolling_auc_traces() (in module seismicrna.graph.trace) iter_root_modules() (seismicrna.core.rna.struct.RNAStructure method) iter_seq_base_bar_traces() (in module seismicrna.graph.trace) iter_seq_base_scatter_traces() (in module seismicrna.graph.trace) iter_seq_line_traces() (in module seismicrna.graph.trace) iter_seqbar_stack_traces() (in module seismicrna.graph.trace) iter_states() (seismicrna.graph.onestruct.StructOneTableGraph method) iter_table_data() (in module seismicrna.export.web) iter_windows() (in module seismicrna.core.batch.index) (in module seismicrna.core.seq.section) (seismicrna.core.batch.muts.SectionMutsBatch method)

J

join_sections() (in module seismicrna.join) JoinClusterMutsDataset (class in seismicrna.cluster.data) JoinClusterReport (class in seismicrna.joinbase.report)

JoinMaskMutsDataset (class in seismicrna.mask.data) JoinMaskReport (class in seismicrna.joinbase.report) JoinMutsDataset (class in seismicrna.joinbase.data)

K

key (seismicrna.core.report.Field attribute) (seismicrna.core.report.OptionField attribute) KEY_DINTER (seismicrna.align.fqunit.FastqUnit attribute) KEY_DMATED (seismicrna.align.fqunit.FastqUnit attribute) KEY_DSINGLE (seismicrna.align.fqunit.FastqUnit attribute) KEY_INTER (seismicrna.align.fqunit.FastqUnit attribute) KEY_MATE1 (seismicrna.align.fqunit.FastqUnit attribute) KEY_MATE2 (seismicrna.align.fqunit.FastqUnit attribute) KEY_MATED (seismicrna.align.fqunit.FastqUnit attribute)

KEY_SINGLE (seismicrna.align.fqunit.FastqUnit attribute) key_to_title() (in module seismicrna.core.report) kind (seismicrna.align.fqunit.FastqUnit property) kind() (seismicrna.table.base.ClustFreqTable class method) (seismicrna.table.base.ClustTable class method) (seismicrna.table.base.MaskTable class method) (seismicrna.table.base.RelTable class method) (seismicrna.table.base.Table class method) kmers() (seismicrna.core.seq.xna.XNA method)

L

label_no_close_muts() (in module seismicrna.core.mu.tests.unbias_test) length (seismicrna.core.seq.section.Section property) lengthen() (seismicrna.relate.aux.cigarop.CigarOp method) level_keys() (seismicrna.core.header.Header class method) level_names() (seismicrna.core.header.Header class method) levels() (seismicrna.core.header.ClustHeader class method) (seismicrna.core.header.Header class method) (seismicrna.core.header.RelHeader class method) list() (seismicrna.core.seq.section.RefSections method) list_batch_nums() (in module seismicrna.core.batch.index) list_clusts() (in module seismicrna.core.header) list_fqs_xams() (in module seismicrna.align.write) list_naturals() (in module seismicrna.core.array) list_order_clusts() (in module seismicrna.core.header) list_orders() (in module seismicrna.core.header) list_orders_clusts() (in module seismicrna.core.header) list_pos() (in module seismicrna.lists.listpos) list_rels() (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsQ53 static method) list_table_files() (seismicrna.graph.base.GraphRunner class method) load() (seismicrna.core.data.Dataset class method) (seismicrna.core.data.LoadedDataset class method) (seismicrna.core.data.MultistepDataset class method) (seismicrna.core.data.TallDataset class method) (seismicrna.core.data.WideDataset class method) (seismicrna.core.io.file.BrickleIO class method) (seismicrna.core.io.file.FileIO class method) (seismicrna.core.report.Report class method) load_all_tables() (in module seismicrna.table.load) load_any_table() (in module seismicrna.table.load)

load_brickle() (in module seismicrna.core.io.brickle) load_ct_structs() (in module seismicrna.fold.load) load_dataset1() (seismicrna.core.data.MultistepDataset class method) load_dataset2() (seismicrna.core.data.MultistepDataset class method) load_datasets() (in module seismicrna.core.data) load_param_dir() (in module seismicrna.sim.relate) load_pclust() (in module seismicrna.sim.clusts) load_pends() (in module seismicrna.sim.ends) load_pmut() (in module seismicrna.sim.muts) load_pos_table() (in module seismicrna.table.load) load_pos_tables() (in module seismicrna.table.load) load_read_table() (in module seismicrna.table.load) load_read_tables() (in module seismicrna.table.load) load_report() (seismicrna.core.data.Dataset class method) load_sections() (in module seismicrna.mask.main) load_table() (in module seismicrna.table.load) load_table_file() (seismicrna.graph.base.GraphWriter class method) load_tables() (in module seismicrna.table.load) LoadedDataset (class in seismicrna.core.data) LoadedMutsDataset (class in seismicrna.core.data) LoadFunction (class in seismicrna.core.data) locate() (seismicrna.core.seq.section.SectionFinder static method) locate_elements() (in module seismicrna.core.array) log_exceptions() (in module seismicrna.core.logs) log_like (seismicrna.cluster.em.EmClustering property) log_like_prev (seismicrna.cluster.em.EmClustering property) logn_exp (seismicrna.cluster.em.EmClustering property) lookup_key() (in module seismicrna.core.report) lookup_title() (in module seismicrna.core.report)

M

make_dict_from_fasta() (in module seismicrna.demult.demultiplex) make_fold_cmd() (in module seismicrna.fold.rnastructure) make_header() (in module seismicrna.core.header) make_index() (in module seismicrna.graph.base) make_path_subject() (in module seismicrna.graph.base) make_pmut_means() (in module seismicrna.sim.muts) make_pmut_means_paired() (in module seismicrna.sim.muts) make_pmut_means_unpaired() (in module seismicrna.sim.muts) make_sequence_objects_from_csv() (in module seismicrna.demult.demultiplex) make_title_action_sample() (in module seismicrna.graph.base) makes_dict_from_fastq() (in module seismicrna.demult.demultiplex) map_nested() (in module seismicrna.core.rna.pair) mapq (seismicrna.relate.py.relate.SamRead attribute) MASK (seismicrna.table.base.PosTable attribute) mask() (seismicrna.mask.write.Masker method) MASK_GU (seismicrna.core.seq.section.Section attribute) mask_gu() (seismicrna.core.seq.section.Section method) MASK_LIST (seismicrna.core.seq.section.Section attribute) mask_list() (seismicrna.core.seq.section.Section method) MASK_NAME (seismicrna.mask.data.MaskMutsDataset attribute) mask_names (seismicrna.core.seq.section.Section property) MASK_POLYA (seismicrna.core.seq.section.Section attribute) mask_polya() (seismicrna.core.seq.section.Section method) MASK_POS_FMUT (seismicrna.mask.write.Masker attribute) MASK_POS_NINFO (seismicrna.mask.write.Masker attribute) MASK_READ_DISCONTIG (seismicrna.mask.write.Masker attribute) MASK_READ_FINFO (seismicrna.mask.write.Masker attribute) MASK_READ_FMUT (seismicrna.mask.write.Masker attribute) MASK_READ_GAP (seismicrna.mask.write.Masker attribute) MASK_READ_INIT (seismicrna.mask.write.Masker attribute) MASK_READ_KEPT (seismicrna.mask.write.Masker attribute) MASK_READ_NCOV (seismicrna.mask.write.Masker attribute) mask_section() (in module seismicrna.mask.write) mask_segment_ends() (in module seismicrna.core.batch.ends) MaskBatchIO (class in seismicrna.mask.io) masked (seismicrna.cluster.em.EmClustering property) masked_bool (seismicrna.core.seq.section.Section property) masked_int (seismicrna.core.seq.section.Section property) masked_zero (seismicrna.core.seq.section.Section property) Masker (class in seismicrna.mask.write) MaskIO (class in seismicrna.mask.io) MaskMutsBatch (class in seismicrna.mask.batch) MaskMutsDataset (class in seismicrna.mask.data) MaskPosTable (class in seismicrna.table.base) MaskPosTableLoader (class in seismicrna.table.load) MaskPosTableWriter (class in seismicrna.table.write) MaskReadBatch (class in seismicrna.mask.batch) MaskReadDataset (class in seismicrna.mask.data) MaskReadTable (class in seismicrna.table.base) MaskReadTableLoader (class in seismicrna.table.load) MaskReadTableWriter (class in seismicrna.table.write) MaskReport (class in seismicrna.mask.report) MaskTable (class in seismicrna.table.base) MaskTabulator (class in seismicrna.table.calc) match_longest_ext() (seismicrna.core.path.Segment method) match_reads_segments() (in module seismicrna.core.batch.ends) matrix (seismicrna.core.batch.muts.SectionMutsBatch property) max_order (seismicrna.cluster.data.ClusterDataset property) (seismicrna.cluster.data.ClusterMutsDataset property) (seismicrna.cluster.data.ClusterReadDataset property) (seismicrna.cluster.data.JoinClusterMutsDataset property) (seismicrna.core.header.ClustHeader property) (seismicrna.core.header.Header property) (seismicrna.core.header.RelHeader property) (seismicrna.table.calc.AvgTabulator property) (seismicrna.table.calc.ClustTabulator property) (seismicrna.table.calc.Tabulator property) MAX_PHRED_ENC (seismicrna.align.fqunit.FastqUnit attribute) max_read (seismicrna.core.batch.read.AllReadBatch property) (seismicrna.core.batch.read.PartialReadBatch property) (seismicrna.core.batch.read.ReadBatch property) merge_nondemult_fqs() (in module seismicrna.align.write) merge_params() (in module seismicrna.core.arg.cli) merge_read_ends() (in module seismicrna.core.batch.ends) merge_segment_ends() (in module seismicrna.core.batch.ends) MergedDataset (class in seismicrna.core.data) MergedMutsDataset (class in seismicrna.core.data) MergedUnbiasDataset (class in seismicrna.core.data) MIN_FIELDS (seismicrna.relate.py.relate.SamRead attribute) min_mut_gap (seismicrna.cluster.data.ClusterMutsDataset property) (seismicrna.core.data.MergedUnbiasDataset property) (seismicrna.core.data.UnbiasDataset property) (seismicrna.joinbase.data.JoinMutsDataset property) (seismicrna.mask.data.MaskMutsDataset property) (seismicrna.mask.data.MaskReadDataset property) min_order (seismicrna.core.header.ClustHeader property) (seismicrna.core.header.Header property) (seismicrna.core.header.RelHeader property) modified() (seismicrna.core.header.Header method) module seismicrna seismicrna.align seismicrna.align.fqops seismicrna.align.fqunit seismicrna.align.main seismicrna.align.report seismicrna.align.sim seismicrna.align.tests seismicrna.align.tests.fqutil_test seismicrna.align.tests.sim_test seismicrna.align.tests.xamgen_test seismicrna.align.write seismicrna.align.xamops seismicrna.cleanfa seismicrna.cleanfa.cleanfa seismicrna.cleanfa.main seismicrna.cluster seismicrna.cluster.addclust seismicrna.cluster.batch seismicrna.cluster.compare seismicrna.cluster.csv seismicrna.cluster.data seismicrna.cluster.delclust seismicrna.cluster.em seismicrna.cluster.io seismicrna.cluster.main seismicrna.cluster.names seismicrna.cluster.report seismicrna.cluster.save seismicrna.cluster.tests seismicrna.cluster.tests.compare_test seismicrna.cluster.tests.em_test seismicrna.cluster.uniq seismicrna.cluster.write seismicrna.core seismicrna.core.arg seismicrna.core.arg.cli seismicrna.core.arg.cmd seismicrna.core.arg.default seismicrna.core.arg.docdef seismicrna.core.array seismicrna.core.batch seismicrna.core.batch.accum seismicrna.core.batch.count seismicrna.core.batch.ends seismicrna.core.batch.index seismicrna.core.batch.muts seismicrna.core.batch.read seismicrna.core.batch.tests seismicrna.core.batch.tests.count_test seismicrna.core.batch.tests.ends_test seismicrna.core.batch.tests.index_test seismicrna.core.batch.tests.muts_test seismicrna.core.data seismicrna.core.extern seismicrna.core.extern.depend seismicrna.core.extern.shell seismicrna.core.extern.tests seismicrna.core.header seismicrna.core.io seismicrna.core.io.batch seismicrna.core.io.brickle seismicrna.core.io.file seismicrna.core.io.seq seismicrna.core.io.tests seismicrna.core.io.tests.file_test seismicrna.core.logs seismicrna.core.mu seismicrna.core.mu.compare seismicrna.core.mu.dim seismicrna.core.mu.frame seismicrna.core.mu.measure seismicrna.core.mu.nan seismicrna.core.mu.scale seismicrna.core.mu.tests seismicrna.core.mu.tests.compare_test seismicrna.core.mu.tests.dim_test seismicrna.core.mu.tests.frame_test seismicrna.core.mu.tests.measure_test seismicrna.core.mu.tests.nan_test seismicrna.core.mu.tests.scale_test seismicrna.core.mu.tests.unbias_test seismicrna.core.mu.unbias seismicrna.core.ngs seismicrna.core.ngs.phred seismicrna.core.ngs.tests seismicrna.core.ngs.tests.phred_test seismicrna.core.ngs.xam seismicrna.core.path seismicrna.core.rel seismicrna.core.rel.code seismicrna.core.rel.pattern seismicrna.core.rel.tests seismicrna.core.rel.tests.code_test seismicrna.core.report seismicrna.core.rna seismicrna.core.rna.base seismicrna.core.rna.convert seismicrna.core.rna.ct seismicrna.core.rna.db seismicrna.core.rna.io seismicrna.core.rna.pair seismicrna.core.rna.profile seismicrna.core.rna.roc seismicrna.core.rna.state seismicrna.core.rna.struct seismicrna.core.rna.tests seismicrna.core.rna.tests.db_test seismicrna.core.rna.tests.pair_test seismicrna.core.run seismicrna.core.seq seismicrna.core.seq.fasta seismicrna.core.seq.refs seismicrna.core.seq.section seismicrna.core.seq.tests seismicrna.core.seq.tests.fasta_test seismicrna.core.seq.tests.section_test seismicrna.core.seq.tests.xna_test seismicrna.core.seq.xna seismicrna.core.stats seismicrna.core.task seismicrna.core.tests seismicrna.core.tests.array_test seismicrna.core.tests.header_test seismicrna.core.tests.stats_test seismicrna.core.tests.version_test seismicrna.core.tmp seismicrna.core.types seismicrna.core.version seismicrna.core.write seismicrna.demult seismicrna.demult.demultiplex seismicrna.demult.main seismicrna.export seismicrna.export.main seismicrna.export.meta seismicrna.export.web seismicrna.fold seismicrna.fold.load seismicrna.fold.main seismicrna.fold.report seismicrna.fold.rnastructure seismicrna.graph seismicrna.graph.aucroll seismicrna.graph.base seismicrna.graph.color seismicrna.graph.corroll seismicrna.graph.delprof seismicrna.graph.giniroll seismicrna.graph.hist seismicrna.graph.histpos seismicrna.graph.histread seismicrna.graph.histrel seismicrna.graph.main seismicrna.graph.onestruct seismicrna.graph.onetable seismicrna.graph.profile seismicrna.graph.rel seismicrna.graph.roc seismicrna.graph.roll seismicrna.graph.scatter seismicrna.graph.snrroll seismicrna.graph.statroll seismicrna.graph.trace seismicrna.graph.twotable seismicrna.join seismicrna.joinbase seismicrna.joinbase.cluster seismicrna.joinbase.data seismicrna.joinbase.report seismicrna.lists seismicrna.lists.listpos seismicrna.lists.lists seismicrna.main seismicrna.mask seismicrna.mask.batch seismicrna.mask.data seismicrna.mask.io seismicrna.mask.main seismicrna.mask.report seismicrna.mask.write seismicrna.pool seismicrna.pool.data seismicrna.pool.main seismicrna.pool.report seismicrna.relate seismicrna.relate.aux seismicrna.relate.aux.cigarop seismicrna.relate.aux.human seismicrna.relate.aux.infer seismicrna.relate.aux.iterread seismicrna.relate.aux.iterrel seismicrna.relate.aux.tests seismicrna.relate.aux.tests.cigarop_test seismicrna.relate.aux.tests.infer_test seismicrna.relate.aux.tests.iterrel_test seismicrna.relate.batch seismicrna.relate.c seismicrna.relate.data seismicrna.relate.io seismicrna.relate.main seismicrna.relate.py seismicrna.relate.py.ambindel seismicrna.relate.py.cigar seismicrna.relate.py.encode seismicrna.relate.py.error seismicrna.relate.py.relate seismicrna.relate.py.tests seismicrna.relate.py.tests.ambindel_test seismicrna.relate.py.tests.cigar_test seismicrna.relate.py.tests.encode_test seismicrna.relate.py.tests.relate_test seismicrna.relate.report seismicrna.relate.sam seismicrna.relate.sim seismicrna.relate.tests seismicrna.relate.tests.sim_test seismicrna.relate.write seismicrna.renumct seismicrna.renumct.main seismicrna.sim seismicrna.sim.clusts seismicrna.sim.ends seismicrna.sim.fastq seismicrna.sim.fold seismicrna.sim.main seismicrna.sim.muts seismicrna.sim.params seismicrna.sim.ref seismicrna.sim.relate seismicrna.sim.tests seismicrna.sim.tests.ends_test seismicrna.sim.total seismicrna.table seismicrna.table.base seismicrna.table.calc seismicrna.table.load seismicrna.table.main seismicrna.table.write seismicrna.test seismicrna.test.main seismicrna.wf

MultiRelsGraph (class in seismicrna.graph.rel) MultiRelsProfileGraph (class in seismicrna.graph.profile) MultistepDataset (class in seismicrna.core.data) mut_bits (seismicrna.core.rel.pattern.HalfRelPattern attribute) muts (seismicrna.core.batch.muts.MutsBatch property) muts() (seismicrna.core.rel.pattern.HalfRelPattern class method) (seismicrna.core.rel.pattern.RelPattern class method) MutsBatch (class in seismicrna.core.batch.muts) MutsBatchIO (class in seismicrna.core.io.batch) MutsDataset (class in seismicrna.core.data)

N

n_batches (seismicrna.mask.write.Masker property) n_data (seismicrna.cluster.em.EmClustering property) n_params (seismicrna.cluster.em.EmClustering property) n_pos_total (seismicrna.cluster.em.EmClustering property) n_pos_unmasked (seismicrna.cluster.em.EmClustering property) n_reads (seismicrna.align.fqunit.FastqUnit property) (seismicrna.relate.sam.XamViewer property) n_reads_discontig (seismicrna.mask.write.Masker property) n_reads_kept (seismicrna.mask.write.Masker property) n_reads_max_fmut (seismicrna.mask.write.Masker property) n_reads_min_finfo (seismicrna.mask.write.Masker property) n_reads_min_gap (seismicrna.mask.write.Masker property) n_reads_min_ncov (seismicrna.mask.write.Masker property) n_reads_premask (seismicrna.mask.write.Masker property) name_batch_attrs() (seismicrna.cluster.data.JoinClusterMutsDataset class method) (seismicrna.joinbase.data.JoinMutsDataset class method) (seismicrna.mask.data.JoinMaskMutsDataset class method) names (seismicrna.core.header.Header property) NarrowDataset (class in seismicrna.core.data) ncols (seismicrna.graph.base.GraphBase property) need_write() (in module seismicrna.core.write) no_close_muts() (in module seismicrna.core.mu.tests.unbias_test) no_nan() (in module seismicrna.core.mu.nan)

none() (seismicrna.core.rel.pattern.HalfRelPattern class method) normalize() (in module seismicrna.core.mu.scale) nos (seismicrna.core.rel.pattern.RelPattern attribute) nrows (seismicrna.graph.base.GraphBase property) num_batches (seismicrna.cluster.uniq.UniqReads property) (seismicrna.core.data.Dataset property) (seismicrna.core.data.LoadedDataset property) (seismicrna.core.data.MultistepDataset property) (seismicrna.core.data.TallDataset property) (seismicrna.core.data.WideDataset property) num_contiguous (seismicrna.core.batch.ends.EndCoords property) num_discontiguous (seismicrna.core.batch.ends.EndCoords property) num_levels() (seismicrna.core.header.Header class method) num_nonuniq (seismicrna.cluster.uniq.UniqReads property) num_reads (seismicrna.cluster.batch.ClusterReadBatch property) (seismicrna.core.batch.ends.EndCoords property) (seismicrna.core.batch.read.ReadBatch property) (seismicrna.core.data.Dataset property) (seismicrna.mask.batch.MaskReadBatch property) (seismicrna.relate.batch.QnamesBatch property) (seismicrna.relate.write.RelationWriter property) num_segments (seismicrna.core.batch.ends.EndCoords property) num_uniq (seismicrna.cluster.uniq.UniqReads property) nums_batches (seismicrna.core.data.TallDataset property)

O

oconv (seismicrna.core.report.Field attribute) (seismicrna.core.report.OptionField attribute) oconv_array_int() (in module seismicrna.core.report) oconv_datetime() (in module seismicrna.core.report) OneRelGraph (class in seismicrna.graph.rel) OneRelProfileGraph (class in seismicrna.graph.profile) OneTableGraph (class in seismicrna.graph.onetable) OneTableRunner (class in seismicrna.graph.onetable) OneTableWriter (class in seismicrna.graph.onetable)

op (seismicrna.relate.aux.cigarop.CigarOp property) op_consumes_read() (in module seismicrna.relate.py.cigar) op_consumes_ref() (in module seismicrna.relate.py.cigar) op_is_mutation() (in module seismicrna.relate.aux.cigarop) open_tmp_sam() (seismicrna.relate.sam.XamViewer method) ops (seismicrna.relate.aux.tests.cigarop_test.TestCigarOp attribute) optional_path() (in module seismicrna.core.arg.cli) OptionField (class in seismicrna.core.report) orders (seismicrna.core.header.Header property)

P

p_ends_given_noclose (seismicrna.table.calc.Tabulator property) paired (seismicrna.relate.data.RelateDataset property) (seismicrna.relate.py.relate.SamFlag attribute) (seismicrna.relate.sam.XamViewer property) pairs (seismicrna.core.rna.struct.RNAStructure property) pairs_to_dict() (in module seismicrna.core.rna.pair) pairs_to_table() (in module seismicrna.core.rna.pair) parallel_grepping() (in module seismicrna.demult.demultiplex) param_defaults() (in module seismicrna.core.arg.docdef) param_docstrs() (in module seismicrna.core.arg.docdef) params() (seismicrna.graph.base.GraphRunner class method) parent (seismicrna.align.fqunit.FastqUnit property) parse() (in module seismicrna.core.path) (seismicrna.core.path.Field method) (seismicrna.core.path.Path method) (seismicrna.core.path.Segment method) parse_all_scores() (seismicrna.align.tests.xamgen_test.TestAlignmentScoreParams method) parse_bowtie2() (in module seismicrna.align.xamops) parse_cigar() (in module seismicrna.relate.py.cigar) parse_ct() (in module seismicrna.core.rna.ct) parse_db() (in module seismicrna.core.rna.db) parse_db_strings() (in module seismicrna.core.rna.db) parse_db_structure() (in module seismicrna.core.rna.db) parse_energy() (in module seismicrna.fold.rnastructure) parse_exp_count_col() (in module seismicrna.cluster.compare) parse_fasta() (in module seismicrna.core.seq.fasta) parse_flagstat() (in module seismicrna.core.ngs.xam) parse_header() (in module seismicrna.core.header) parse_idxstats() (in module seismicrna.core.ngs.xam) parse_join_clusts_file() (in module seismicrna.joinbase.cluster) parse_path() (seismicrna.core.io.file.FileIO class method) parse_ref_header() (in module seismicrna.core.ngs.xam) parse_refs_metadata() (in module seismicrna.export.meta) parse_rnastructure_ct_title() (in module seismicrna.fold.rnastructure) parse_samples_metadata() (in module seismicrna.export.meta) parse_scores() (seismicrna.align.tests.xamgen_test.TestAlignmentScoreParams static method) parse_stdout_count_fastq_reads() (in module seismicrna.align.fqunit) parse_top_separate() (in module seismicrna.core.path) parse_version() (in module seismicrna.core.version) PartialMutsBatch (class in seismicrna.core.batch.muts) PartialReadBatch (class in seismicrna.core.batch.read) PartialTabulator (class in seismicrna.table.calc) Path (class in seismicrna.core.path) path (seismicrna.table.base.Table property) path_field_values() (seismicrna.core.io.file.FileIO method) path_fields (seismicrna.table.base.Table property) path_fields() (seismicrna.core.io.file.FileIO class method) path_matches() (in module seismicrna.core.path) path_segs() (seismicrna.pool.report.PoolReport class method) (seismicrna.table.base.FreqTable class method) (seismicrna.table.base.PosTable class method) (seismicrna.table.base.ReadTable class method) (seismicrna.table.base.Table class method) path_subject (seismicrna.graph.base.GraphBase property) (seismicrna.graph.onestruct.StructOneTableGraph property) (seismicrna.graph.onetable.OneTableGraph property) (seismicrna.graph.twotable.TwoTableGraph property)

path_subject1 (seismicrna.graph.twotable.TwoTableGraph property) path_subject2 (seismicrna.graph.twotable.TwoTableGraph property) PathError PathTypeError PathValueError pattern (seismicrna.cluster.data.ClusterMutsDataset property) (seismicrna.cluster.data.ClusterReadDataset property) (seismicrna.core.data.Dataset property) (seismicrna.core.data.MergedDataset property) (seismicrna.mask.data.MaskMutsDataset property) (seismicrna.mask.data.MaskReadDataset property) (seismicrna.relate.data.QnamesDataset property) (seismicrna.relate.data.RelateDataset property) PATTERN_KEY (seismicrna.mask.write.Masker attribute) patterns (seismicrna.core.rel.pattern.HalfRelPattern property) phred_arg (seismicrna.align.fqunit.FastqUnit property) pict() (seismicrna.core.seq.xna.DNA class method) (seismicrna.core.seq.xna.RNA class method) (seismicrna.core.seq.xna.XNA class method) picto (seismicrna.core.seq.xna.XNA property) pool_samples() (in module seismicrna.pool.main) PoolDataset (class in seismicrna.pool.data) PoolReport (class in seismicrna.pool.report) pos (seismicrna.relate.py.relate.SamRead attribute) pos_dtype (seismicrna.core.batch.ends.EndCoords property) pos_gu (seismicrna.mask.write.Masker property) pos_header (seismicrna.table.calc.Tabulator property) pos_index (seismicrna.core.batch.muts.SectionMutsBatch property) pos_kept (seismicrna.mask.data.MaskReadDataset property) (seismicrna.mask.write.Masker property) pos_list (seismicrna.mask.write.Masker property) pos_max_fmut (seismicrna.mask.write.Masker property) pos_min_ninfo (seismicrna.mask.write.Masker property) pos_nums (seismicrna.core.batch.muts.MutsBatch property) pos_polya (seismicrna.mask.write.Masker property) PosGraphRunner (class in seismicrna.graph.base) PosGraphWriter (class in seismicrna.graph.base) PosHistogramGraph (class in seismicrna.graph.histpos) PosHistogramRunner (class in seismicrna.graph.histpos) PosHistogramWriter (class in seismicrna.graph.histpos) PosTable (class in seismicrna.table.base) PosTableLoader (class in seismicrna.table.load) PosTableWriter (class in seismicrna.table.write) predicate (seismicrna.graph.base.GraphBase property) (seismicrna.graph.corroll.RollingCorrelationGraph property) (seismicrna.graph.roll.RollingGraph property) profile (seismicrna.core.rna.profile.RNAProfile property) profile_names (seismicrna.graph.aucroll.RollingAUCGraph property) (seismicrna.graph.roc.ROCGraph property) ProfileGraph (class in seismicrna.graph.profile) ProfilePosTable (class in seismicrna.table.base) ProfileRunner (class in seismicrna.graph.profile) ProfileWriter (class in seismicrna.graph.profile) ptrn_fancy (seismicrna.core.rel.pattern.HalfRelPattern attribute) ptrn_plain (seismicrna.core.rel.pattern.HalfRelPattern attribute) PURPLE (seismicrna.core.logs.AnsiCode attribute)

Q

qname (seismicrna.relate.py.relate.SamRead attribute) QnamesBatch (class in seismicrna.relate.batch) QnamesBatchIO (class in seismicrna.relate.io) QnamesDataset (class in seismicrna.relate.data) qual (seismicrna.relate.py.relate.SamRead attribute) quick_unbias (seismicrna.cluster.data.ClusterMutsDataset property) (seismicrna.core.data.MergedUnbiasDataset property) (seismicrna.core.data.UnbiasDataset property) (seismicrna.mask.data.MaskMutsDataset property) (seismicrna.mask.data.MaskReadDataset property)

quick_unbias_thresh (seismicrna.cluster.data.ClusterMutsDataset property) (seismicrna.core.data.MergedUnbiasDataset property) (seismicrna.core.data.UnbiasDataset property) (seismicrna.mask.data.MaskMutsDataset property) (seismicrna.mask.data.MaskReadDataset property)

R

rand_dirichlet_alpha() (in module seismicrna.core.tests.stats_test) randdir() (in module seismicrna.core.path) randname() (in module seismicrna.core.path) random() (seismicrna.core.seq.xna.XNA class method) random_params() (seismicrna.core.mu.tests.unbias_test.TestQuickUnbias static method) range (seismicrna.core.seq.section.Section property) (seismicrna.table.base.PosTable property) range_int (seismicrna.core.seq.section.Section property) (seismicrna.table.base.PosTable property) range_one (seismicrna.core.seq.section.Section property) rank (seismicrna.relate.py.ambindel.Deletion property) (seismicrna.relate.py.ambindel.Indel property) (seismicrna.relate.py.ambindel.Insertion property) rc (seismicrna.core.seq.xna.XNA property) read_bases (seismicrna.core.rel.pattern.HalfRelPattern attribute) read_dtype (seismicrna.core.batch.read.ReadBatch property) read_end3s (seismicrna.core.batch.ends.EndCoords property) read_end3s_zero (seismicrna.cluster.uniq.UniqReads property) read_end5s (seismicrna.core.batch.ends.EndCoords property) read_end5s_zero (seismicrna.cluster.uniq.UniqReads property) read_end_counts (seismicrna.core.batch.muts.MutsBatch property) read_header (seismicrna.table.calc.Tabulator property) read_indexes (seismicrna.core.batch.read.AllReadBatch property) (seismicrna.core.batch.read.PartialReadBatch property) (seismicrna.core.batch.read.ReadBatch property) read_name() (in module seismicrna.relate.sam) read_nums (seismicrna.cluster.batch.ClusterReadBatch property) (seismicrna.core.batch.read.AllReadBatch property) (seismicrna.core.batch.read.ReadBatch property) (seismicrna.mask.batch.MaskReadBatch property) read_weights (seismicrna.cluster.batch.ClusterMutsBatch property) (seismicrna.core.batch.muts.MutsBatch property) (seismicrna.mask.batch.MaskMutsBatch property) (seismicrna.relate.batch.RelateBatch property) ReadBatch (class in seismicrna.core.batch.read) ReadBatchIO (class in seismicrna.core.io.batch) ReadGraphRunner (class in seismicrna.graph.base) ReadGraphWriter (class in seismicrna.graph.base) ReadHistogramGraph (class in seismicrna.graph.histread) ReadHistogramRunner (class in seismicrna.graph.histread) ReadHistogramWriter (class in seismicrna.graph.histread) reads (seismicrna.table.base.ReadTable property) reads_noclose_muts() (seismicrna.core.batch.muts.SectionMutsBatch method) reads_per_pos() (seismicrna.core.batch.muts.SectionMutsBatch method) ReadTable (class in seismicrna.table.base) ReadTableLoader (class in seismicrna.table.load) ReadTableWriter (class in seismicrna.table.write) realign_cmd() (in module seismicrna.align.xamops) recast_file_path() (in module seismicrna.core.io.file) RED (seismicrna.core.logs.AnsiCode attribute) ref (seismicrna.cluster.uniq.UniqReads property) (seismicrna.core.data.Dataset property) (seismicrna.core.data.LoadedDataset property) (seismicrna.core.data.MergedDataset property) (seismicrna.core.data.MultistepDataset property) (seismicrna.core.rna.base.RNASection property) (seismicrna.graph.base.GraphBase property) (seismicrna.graph.onetable.OneTableGraph property) (seismicrna.graph.twotable.TwoTableGraph property) (seismicrna.relate.sam.XamViewer property) (seismicrna.relate.write.RelationWriter property) (seismicrna.table.base.Table property) (seismicrna.table.calc.Tabulator property) (seismicrna.table.load.TableLoader property) (seismicrna.table.write.TableWriter property) ref_bases (seismicrna.core.rel.pattern.HalfRelPattern attribute) ref_header_cmd() (in module seismicrna.core.ngs.xam) ref_sect (seismicrna.core.seq.section.Section property) ref_to_alignments() (in module seismicrna.relate.aux.iterread) RefIO (class in seismicrna.core.io.file) reflen (seismicrna.core.data.MutsDataset property) reframe() (in module seismicrna.core.mu.frame) reframe_like() (in module seismicrna.core.mu.frame) refs (seismicrna.core.seq.section.RefSections property) refs() (seismicrna.core.rel.pattern.HalfRelPattern class method) RefSections (class in seismicrna.core.seq.section) refseq (seismicrna.core.data.LoadedMutsDataset property) (seismicrna.core.data.MergedMutsDataset property) (seismicrna.core.data.MultistepDataset property) (seismicrna.core.data.MutsDataset property) (seismicrna.core.io.seq.RefseqIO property) (seismicrna.table.base.Table property) (seismicrna.table.calc.Tabulator property) refseq_file() (seismicrna.relate.report.RelateReport method) refseq_file_auto_fields() (in module seismicrna.relate.report) refseq_file_path() (in module seismicrna.relate.report) refseq_file_seg_types() (in module seismicrna.relate.report) RefseqIO (class in seismicrna.core.io.seq) RefseqReport (class in seismicrna.core.report) RefSeqs (class in seismicrna.core.seq.refs) regular_grepping() (in module seismicrna.demult.demultiplex) rel_name (seismicrna.graph.rel.OneRelGraph property) rel_names (seismicrna.graph.base.GraphBase property) (seismicrna.graph.rel.MultiRelsGraph property) (seismicrna.graph.rel.OneRelGraph property) REL_TOL (seismicrna.core.mu.tests.unbias_test.TestQuickUnbias attribute) relate() (seismicrna.relate.py.tests.relate_test.TestFindRelsLine static method) RelateBatch (class in seismicrna.relate.batch) RelateBatchIO (class in seismicrna.relate.io) RelateDataset (class in seismicrna.relate.data) RelateError RelateIO (class in seismicrna.relate.io) RelateNotImplementedError RelateReport (class in seismicrna.relate.report) RelateTabulator (class in seismicrna.table.calc) RelateValueError relationships (seismicrna.graph.base.GraphBase property) RelationWriter (class in seismicrna.relate.write) RelClustHeader (class in seismicrna.core.header) RelColorMap (class in seismicrna.graph.color) release_to_out() (in module seismicrna.core.tmp) RelHeader (class in seismicrna.core.header) RelHistogramGraph (class in seismicrna.graph.histrel) RelHistogramRunner (class in seismicrna.graph.histrel) RelHistogramWriter (class in seismicrna.graph.histrel)

RelPattern (class in seismicrna.core.rel.pattern) RelPosTable (class in seismicrna.table.base) RelPosTableLoader (class in seismicrna.table.load) RelPosTableWriter (class in seismicrna.table.write) RelReadTable (class in seismicrna.table.base) RelReadTableLoader (class in seismicrna.table.load) RelReadTableWriter (class in seismicrna.table.write) rels (seismicrna.core.header.RelHeader property) rels_per_pos (seismicrna.core.batch.muts.SectionMutsBatch property) rels_per_read (seismicrna.core.batch.muts.SectionMutsBatch property) RelTable (class in seismicrna.table.base) RelTypeTable (class in seismicrna.table.base) RelTypeTableLoader (class in seismicrna.table.load) relvecs_to_sam_file() (in module seismicrna.align.sim) relvecs_to_sam_lines() (in module seismicrna.align.sim) remove_mask() (seismicrna.core.seq.section.Section method) remove_nan() (in module seismicrna.core.mu.nan) removes_nan() (in module seismicrna.core.mu.nan) rename_columns() (in module seismicrna.graph.roc) renumber_ct() (in module seismicrna.core.rna.io) renumber_from() (seismicrna.core.rna.base.RNASection method) (seismicrna.core.seq.section.Section method) renumber_pairs() (in module seismicrna.core.rna.pair) Report (class in seismicrna.core.report) report_path_auto_fields (seismicrna.core.data.LoadFunction property) report_path_seg_types (seismicrna.core.data.LoadFunction property) require_data_path() (in module seismicrna.fold.rnastructure) require_dependency() (in module seismicrna.core.extern.depend) resample() (seismicrna.table.base.PosTable method) reset() (seismicrna.relate.py.ambindel.Indel method) resolve_or_analyze_multigrepped_reads() (in module seismicrna.demult.demultiplex) retitle_ct() (in module seismicrna.fold.rnastructure) rev (seismicrna.relate.py.relate.SamFlag attribute) reverse_compliment() (in module seismicrna.demult.demultiplex) RNA (class in seismicrna.core.seq.xna) Rna2dPart (class in seismicrna.core.rna.struct) Rna2dStem (class in seismicrna.core.rna.struct) Rna2dStemLoop (class in seismicrna.core.rna.struct) RnaJunction (class in seismicrna.core.rna.struct) rname (seismicrna.relate.py.relate.SamRead attribute) RNAProfile (class in seismicrna.core.rna.profile) RNASection (class in seismicrna.core.rna.base) RNAState (class in seismicrna.core.rna.state) RNAStructure (class in seismicrna.core.rna.struct) roc (seismicrna.core.rna.state.RNAState property) ROCGraph (class in seismicrna.graph.roc) ROCRunner (class in seismicrna.graph.roc) ROCWriter (class in seismicrna.graph.roc) rolling_auc() (seismicrna.core.rna.state.RNAState method) RollingAUCGraph (class in seismicrna.graph.aucroll) RollingAUCRunner (class in seismicrna.graph.aucroll) RollingAUCWriter (class in seismicrna.graph.aucroll) RollingCorrelationGraph (class in seismicrna.graph.corroll) RollingCorrelationRunner (class in seismicrna.graph.corroll) RollingCorrelationWriter (class in seismicrna.graph.corroll) RollingGiniGraph (class in seismicrna.graph.giniroll) RollingGiniRunner (class in seismicrna.graph.giniroll) RollingGiniWriter (class in seismicrna.graph.giniroll) RollingGraph (class in seismicrna.graph.roll) RollingRunner (class in seismicrna.graph.roll) RollingSNRGraph (class in seismicrna.graph.snrroll) RollingSNRRunner (class in seismicrna.graph.snrroll) RollingSNRWriter (class in seismicrna.graph.snrroll) RollingStatGraph (class in seismicrna.graph.statroll) RollingStatRunner (class in seismicrna.graph.statroll) RollingStatWriter (class in seismicrna.graph.statroll) roots (seismicrna.core.rna.struct.RNAStructure property) row_index (seismicrna.graph.base.GraphBase property) (seismicrna.graph.onetable.OneTableGraph property) (seismicrna.graph.twotable.TwoTableGraph property) row_titles (seismicrna.graph.base.GraphBase property) rt() (seismicrna.core.seq.xna.RNA method) run() (in module seismicrna.align.main) (in module seismicrna.cleanfa.main) (in module seismicrna.cluster.addclust) (in module seismicrna.cluster.delclust) (in module seismicrna.cluster.main) (in module seismicrna.export.main) (in module seismicrna.fold.main) (in module seismicrna.join) (in module seismicrna.lists.listpos) (in module seismicrna.mask.main) (in module seismicrna.pool.main) (in module seismicrna.relate.main) (in module seismicrna.renumct.main) (in module seismicrna.sim.clusts) (in module seismicrna.sim.ends) (in module seismicrna.sim.fastq) (in module seismicrna.sim.fold) (in module seismicrna.sim.muts) (in module seismicrna.sim.params) (in module seismicrna.sim.ref) (in module seismicrna.sim.relate) (in module seismicrna.sim.total) (in module seismicrna.table.main) (in module seismicrna.test.main) (in module seismicrna.wf) (seismicrna.cleanfa.cleanfa.FastaCleaner method) (seismicrna.cluster.em.EmClustering method) (seismicrna.graph.base.GraphRunner class method) (seismicrna.graph.onetable.OneTableRunner class method) (seismicrna.graph.twotable.TwoTableRunner class method) run_cmd() (in module seismicrna.core.extern.shell) run_ct_to_db() (in module seismicrna.core.rna.convert) run_db_to_ct() (in module seismicrna.core.rna.convert) run_dm() (in module seismicrna.demult.main) run_fastqc() (in module seismicrna.align.fqops) run_func() (in module seismicrna.core.run) run_max_order() (in module seismicrna.cluster.write) run_multi_greps() (in module seismicrna.demult.demultiplex) run_order() (in module seismicrna.cluster.write) run_orders() (in module seismicrna.cluster.write) run_seqkit_grep() (in module seismicrna.demult.demultiplex) run_seqkit_grep_function() (in module seismicrna.demult.demultiplex) run_struct() (in module seismicrna.sim.muts) RunOrderResults (class in seismicrna.cluster.compare)

S

sam_header() (in module seismicrna.align.sim) SamFlag (class in seismicrna.relate.py.relate) sample (seismicrna.core.data.Dataset property) (seismicrna.core.data.LoadedDataset property) (seismicrna.core.data.MultistepDataset property) (seismicrna.core.data.TallDataset property) (seismicrna.core.data.WideDataset property) (seismicrna.graph.base.GraphBase property) (seismicrna.graph.onetable.OneTableGraph property) (seismicrna.graph.twotable.TwoTableGraph property) (seismicrna.relate.sam.XamViewer property) (seismicrna.relate.write.RelationWriter property) (seismicrna.table.base.Table property) (seismicrna.table.calc.Tabulator property) (seismicrna.table.load.TableLoader property) (seismicrna.table.write.TableWriter property) sample1 (seismicrna.graph.twotable.TwoTableGraph property) sample2 (seismicrna.graph.twotable.TwoTableGraph property) samples (seismicrna.core.data.TallDataset property) SamRead (class in seismicrna.relate.py.relate) sanitize() (in module seismicrna.core.path) sanitize_muts() (in module seismicrna.core.batch.muts) sanitize_segment_ends() (in module seismicrna.core.batch.ends) sanitize_values() (in module seismicrna.core.array) save() (seismicrna.core.io.file.BrickleIO method) (seismicrna.core.io.file.FileIO method) (seismicrna.core.report.Report method) save_brickle() (in module seismicrna.core.io.brickle) ScatterPlotGraph (class in seismicrna.graph.scatter) ScatterPlotRunner (class in seismicrna.graph.scatter) ScatterPlotWriter (class in seismicrna.graph.scatter) second (seismicrna.relate.py.relate.SamFlag attribute) sect (seismicrna.core.data.Dataset property) (seismicrna.core.data.LoadedDataset property) (seismicrna.core.data.LoadedMutsDataset property) (seismicrna.core.data.MultistepDataset property) (seismicrna.core.data.TallDataset property) (seismicrna.core.data.WideDataset property) (seismicrna.core.rna.base.RNASection property) (seismicrna.graph.base.GraphBase property) (seismicrna.graph.onetable.OneTableGraph property) (seismicrna.graph.twotable.TwoTableGraph property) (seismicrna.table.base.Table property) (seismicrna.table.load.TableLoader property) (seismicrna.table.write.TableWriter property) SectIO (class in seismicrna.core.io.file) Section (class in seismicrna.core.seq.section) section (seismicrna.cluster.data.ClusterMutsDataset property) (seismicrna.core.data.MutsDataset property) (seismicrna.core.data.NarrowDataset property) (seismicrna.core.data.WideDataset property) (seismicrna.core.rna.struct.Rna2dStemLoop property) (seismicrna.mask.data.MaskMutsDataset property) (seismicrna.table.base.PosTable property) (seismicrna.table.calc.Tabulator property) section3 (seismicrna.core.rna.struct.Rna2dStem property) section5 (seismicrna.core.rna.struct.Rna2dStem property) section_end5 (seismicrna.cluster.em.EmClustering property) SectionFinder (class in seismicrna.core.seq.section) SectionMutsBatch (class in seismicrna.core.batch.muts) sections (seismicrna.core.seq.section.RefSections property) SectionTuple (in module seismicrna.core.seq.section) sects (seismicrna.core.data.WideDataset property) seg_end3s (seismicrna.core.batch.ends.EndCoords property) seg_end3s_zero (seismicrna.cluster.uniq.UniqReads property) seg_end5s (seismicrna.core.batch.ends.EndCoords property) seg_end5s_zero (seismicrna.cluster.uniq.UniqReads property) seg_types (seismicrna.align.fqunit.FastqUnit property) seg_types() (seismicrna.core.io.file.FileIO class method) Segment (class in seismicrna.core.path) seismic-+addclust command line option --brotli-level --max-clusters --max-procs --parallel --serial --tmp-pfx -k -t INPUT_PATH seismic-+cleanfa command line option --force --inplace --max-procs --newfile --no-force --out-dir --parallel --serial -o INPUT_PATH seismic-+delclust command line option --brotli-level --max-clusters --max-procs --parallel --serial --tmp-pfx -k -t INPUT_PATH seismic-+listpos command line option --complement --force --max-fmut-pos --max-procs --no-complement --no-force --parallel --serial INPUT_PATH seismic-+renumct command line option --ct-pos-5 --force --inplace --max-procs --newfile --no-force --out-dir --parallel --serial -c -o seismic-+sim-clusts command line option --clust-conc --ct-file --force --max-procs --no-force --parallel --serial -c -i seismic-+sim-ends command line option --ct-file --end3-fmean --ends-var --force --insert-fmean --max-procs --no-force --parallel --serial -3 -e -i -l seismic-+sim-fastq command line option --force --fq-gzip --fq-text --max-procs --min-mut-gap --no-force --num-reads --paired-end --parallel --param-dir --profile-name --read-length --reverse-fraction --sample --serial --single-end -d -n -P -s INPUT_PATH seismic-+sim-fold command line option --erase-tmp --fold-constraint --fold-coords --fold-max --fold-md --fold-mfe --fold-percent --fold-primers --fold-sections-file --fold-sub --fold-temp --force --keep-tmp --max-procs --no-force --parallel --profile-name --serial --sim-dir --tmp-pfx -f -o -P -t FASTA seismic-+sim-muts command line option --ct-file --force --max-procs --no-force --parallel --pmut-paired --pmut-unpaired --serial --vmut-paired --vmut-unpaired -i -p -u -v -w seismic-+sim-params command line option --clust-conc --ct-file --end3-fmean --ends-var --force --insert-fmean --max-procs --no-force --parallel --pmut-paired --pmut-unpaired --serial --vmut-paired --vmut-unpaired -3 -c -e -i -l -p -u -v -w seismic-+sim-ref command line option --force --no-force --ref --reflen --refs --sim-dir -N -o -R -r seismic-+sim-relate command line option --batch-size --brotli-level --force --max-procs --min-mut-gap --no-force --num-reads --paired-end --parallel --param-dir --profile-name --read-length --reverse-fraction --sample --serial --single-end -d -n -P -s seismic-+sim-total command line option --clust-conc --end3-fmean --ends-var --erase-tmp --fold-constraint --fold-coords --fold-max --fold-md --fold-mfe --fold-percent --fold-primers --fold-sections-file --fold-sub --fold-temp --force --fq-gzip --fq-text --insert-fmean --keep-tmp --max-procs --min-mut-gap --no-force --num-reads --paired-end --parallel --pmut-paired --pmut-unpaired --profile-name --read-length --ref --reflen --refs --reverse-fraction --sample --serial --sim-dir --single-end --tmp-pfx --vmut-paired --vmut-unpaired -3 -c -e -f -l -n -N -o -P -p -R -r -s -t -u -v -w seismic-+test command line option --verbose -v seismic-align command line option --bt2-contain --bt2-D --bt2-discordant --bt2-dovetail --bt2-dpad --bt2-end-to-end --bt2-gbar --bt2-I --bt2-i --bt2-L --bt2-local --bt2-mixed --bt2-no-contain --bt2-no-discordant --bt2-no-dovetail --bt2-no-mixed --bt2-no-un --bt2-orient --bt2-R --bt2-score-min-e2e --bt2-score-min-loc --bt2-un --bt2-X --cut --cut-a1 --cut-a2 --cut-discard-trimmed --cut-discard-untrimmed --cut-e --cut-g1 --cut-g2 --cut-indels --cut-keep-trimmed --cut-keep-untrimmed --cut-m --cut-nextseq --cut-no-indels --cut-no-nextseq --cut-O --cut-q1 --cut-q2 --dmfastqx --dmfastqy --dmfastqz --erase-tmp --f1r2-minus --f1r2-plus --fastqc --fastqx --fastqy --fastqz --force --keep-tmp --max-procs --min-mapq --min-reads --minus-label --mix-strands --no-cut --no-fastqc --no-force --out-dir --parallel --phred-enc --qc-extract --qc-no-extract --sep-strands --serial --tmp-pfx -N -o -t -x -X -y -Y -z -Z FASTA seismic-cluster command line option --brotli-level --em-runs --em-thresh --erase-tmp --force --keep-tmp --max-clusters --max-em-iter --max-procs --min-em-iter --no-force --parallel --serial --tmp-pfx -e -k -t INPUT_PATH seismic-demult command line option --barcode-end --barcode-start --clipped --demulti-overwrite --erase-tmp --fastqx --index-tolerance --keep-tmp --mismatch-tolerence --out-dir --parallel-demultiplexing --phred-enc --refs-meta --tmp-pfx -o -R -t -x FASTA seismic-fold command line option --erase-tmp --fold-constraint --fold-coords --fold-full --fold-max --fold-md --fold-mfe --fold-percent --fold-primers --fold-sections-file --fold-sub --fold-table --fold-temp --force --keep-tmp --max-procs --no-force --parallel --quantile --serial --tmp-pfx -f -q -t INPUT_PATH seismic-graph-aucroll command line option --cgroup --csv --fold-coords --fold-full --fold-primers --fold-sections-file --fold-table --force --html --max-procs --no-csv --no-force --no-html --no-pdf --no-png --no-svg --parallel --pdf --png --quantile --rels --serial --struct-file --svg --use-count --use-ratio --window --winmin -f -n -q -r -w INPUT_PATH seismic-graph-corroll command line option --cgroup --comppair --compself --csv --force --html --max-procs --metric --no-comppair --no-compself --no-csv --no-force --no-html --no-pdf --no-png --no-svg --out-dir --parallel --pdf --png --quantile --rels --serial --svg --use-count --use-ratio --window --winmin -m -n -o -q -r -w INPUT_PATH seismic-graph-delprof command line option --cgroup --comppair --compself --csv --force --html --max-procs --no-comppair --no-compself --no-csv --no-force --no-html --no-pdf --no-png --no-svg --out-dir --parallel --pdf --png --quantile --rels --serial --svg --use-count --use-ratio -o -q -r INPUT_PATH seismic-graph-histpos command line option --cgroup --csv --force --hist-bins --hist-margin --html --max-procs --no-csv --no-force --no-html --no-pdf --no-png --no-svg --parallel --pdf --png --quantile --rels --serial --svg --use-count --use-ratio -q -r INPUT_PATH seismic-graph-histread command line option --cgroup --csv --force --hist-bins --hist-margin --html --max-procs --no-csv --no-force --no-html --no-pdf --no-png --no-svg --parallel --pdf --png --quantile --rels --serial --svg --use-count --use-ratio -q -r INPUT_PATH seismic-graph-profile command line option --cgroup --csv --force --html --max-procs --no-csv --no-force --no-html --no-pdf --no-png --no-svg --parallel --pdf --png --quantile --rels --serial --svg --use-count --use-ratio -q -r INPUT_PATH seismic-graph-roc command line option --cgroup --csv --fold-coords --fold-full --fold-primers --fold-sections-file --fold-table --force --html --max-procs --no-csv --no-force --no-html --no-pdf --no-png --no-svg --parallel --pdf --png --quantile --rels --serial --struct-file --svg --use-count --use-ratio -f -q -r INPUT_PATH seismic-graph-scatter command line option --cgroup --comppair --compself --csv --force --html --max-procs --no-comppair --no-compself --no-csv --no-force --no-html --no-pdf --no-png --no-svg --out-dir --parallel --pdf --png --quantile --rels --serial --svg --use-count --use-ratio -o -q -r INPUT_PATH seismic-mask command line option --brotli-level --erase-tmp --exact-unbias --force --keep-del --keep-discontig --keep-gu --keep-ins --keep-tmp --mask-coords --mask-del --mask-discontig --mask-gu --mask-ins --mask-mut --mask-polya --mask-pos --mask-pos-file --mask-primers --mask-sections-file --max-fmut-pos --max-fmut-read --max-procs --min-finfo-read --min-mut-gap --min-ncov-read --min-ninfo-pos --no-force --parallel --primer-gap --quick-unbias --quick-unbias-thresh --serial --tmp-pfx -c -p -s -t INPUT_PATH seismic-relate command line option --ambindel --batch-size --brotli-level --clip-end3 --clip-end5 --erase-tmp --force --keep-tmp --max-procs --min-mapq --min-phred --min-reads --no-ambindel --no-force --no-overhangs --out-dir --overhangs --parallel --phred-enc --serial --tmp-pfx -3 -5 -N -o -t FASTA INPUT_PATH

seismic-table command line option --force --max-procs --no-force --no-table-clust --no-table-pos --no-table-read --parallel --serial --table-clust --table-pos --table-read INPUT_PATH seismic-wf command line option --all-pos --ambindel --barcode-end --barcode-start --batch-size --brotli-level --bt2-contain --bt2-D --bt2-discordant --bt2-dovetail --bt2-dpad --bt2-end-to-end --bt2-gbar --bt2-I --bt2-i --bt2-L --bt2-local --bt2-mixed --bt2-no-contain --bt2-no-discordant --bt2-no-dovetail --bt2-no-mixed --bt2-no-un --bt2-orient --bt2-R --bt2-score-min-e2e --bt2-score-min-loc --bt2-un --bt2-X --cgroup --clip-end3 --clip-end5 --clipped --csv --cut --cut-a1 --cut-a2 --cut-discard-trimmed --cut-discard-untrimmed --cut-e --cut-g1 --cut-g2 --cut-indels --cut-keep-trimmed --cut-keep-untrimmed --cut-m --cut-nextseq --cut-no-indels --cut-no-nextseq --cut-O --cut-q1 --cut-q2 --demult-off --demult-on --demulti-overwrite --dmfastqx --dmfastqy --dmfastqz --em-runs --em-thresh --erase-tmp --exact-unbias --export --f1r2-minus --f1r2-plus --fastqc --fastqx --fastqy --fastqz --fold --fold-constraint --fold-coords --fold-full --fold-max --fold-md --fold-mfe --fold-percent --fold-primers --fold-sections-file --fold-sub --fold-table --fold-temp --force --graph-aucroll --graph-giniroll --graph-mhist --graph-mprof --graph-ncov --graph-roc --graph-tmprof --hist-bins --hist-margin --html --index-tolerance --join-clusts --joined --keep-del --keep-discontig --keep-gu --keep-ins --keep-tmp --mask-coords --mask-del --mask-discontig --mask-gu --mask-ins --mask-mut --mask-polya --mask-pos --mask-pos-file --mask-primers --mask-sections-file --max-clusters --max-em-iter --max-fmut-pos --max-fmut-read --max-procs --min-em-iter --min-finfo-read --min-mapq --min-mut-gap --min-ncov-read --min-ninfo-pos --min-phred --min-reads --minus-label --mismatch-tolerence --mix-strands --no-ambindel --no-csv --no-cut --no-export --no-fastqc --no-fold --no-force --no-graph-aucroll --no-graph-giniroll --no-graph-mhist --no-graph-mprof --no-graph-ncov --no-graph-roc --no-graph-tmprof --no-html --no-overhangs --no-pdf --no-png --no-svg --no-table-clust --no-table-pos --no-table-read --out-dir --overhangs --parallel --parallel-demultiplexing --pdf --phred-enc --png --pool --primer-gap --qc-extract --qc-no-extract --quantile --quick-unbias --quick-unbias-thresh --refs-meta --samples-meta --sep-strands --serial --struct-file --svg --table-clust --table-pos --table-read --tmp-pfx --unmasked-pos --window --winmin -3 -5 -c -e -f -J -j -k -N -n -o -P -p -q -R -s -S -t -w -x -X -y -Y -z -Z FASTA INPUT_PATH seismicrna module seismicrna.align module seismicrna.align.fqops module seismicrna.align.fqunit module seismicrna.align.main module seismicrna.align.report module seismicrna.align.sim module seismicrna.align.tests module seismicrna.align.tests.fqutil_test module seismicrna.align.tests.sim_test module seismicrna.align.tests.xamgen_test module seismicrna.align.write module seismicrna.align.xamops module seismicrna.cleanfa module seismicrna.cleanfa.cleanfa module seismicrna.cleanfa.main module seismicrna.cluster module seismicrna.cluster.addclust module seismicrna.cluster.batch module seismicrna.cluster.compare module seismicrna.cluster.csv module seismicrna.cluster.data module seismicrna.cluster.delclust module seismicrna.cluster.em module seismicrna.cluster.io module seismicrna.cluster.main module seismicrna.cluster.names module seismicrna.cluster.report module seismicrna.cluster.save module seismicrna.cluster.tests module seismicrna.cluster.tests.compare_test module seismicrna.cluster.tests.em_test module seismicrna.cluster.uniq module seismicrna.cluster.write module seismicrna.core module seismicrna.core.arg module seismicrna.core.arg.cli module seismicrna.core.arg.cmd module seismicrna.core.arg.default module seismicrna.core.arg.docdef module seismicrna.core.array module seismicrna.core.batch module seismicrna.core.batch.accum module seismicrna.core.batch.count module seismicrna.core.batch.ends module seismicrna.core.batch.index module seismicrna.core.batch.muts module seismicrna.core.batch.read module seismicrna.core.batch.tests module seismicrna.core.batch.tests.count_test module seismicrna.core.batch.tests.ends_test module seismicrna.core.batch.tests.index_test module seismicrna.core.batch.tests.muts_test module seismicrna.core.data module seismicrna.core.extern module seismicrna.core.extern.depend module seismicrna.core.extern.shell module seismicrna.core.extern.tests module seismicrna.core.header module seismicrna.core.io module seismicrna.core.io.batch module seismicrna.core.io.brickle module seismicrna.core.io.file module seismicrna.core.io.seq module seismicrna.core.io.tests module seismicrna.core.io.tests.file_test module seismicrna.core.logs module seismicrna.core.mu module seismicrna.core.mu.compare module seismicrna.core.mu.dim module seismicrna.core.mu.frame module seismicrna.core.mu.measure module seismicrna.core.mu.nan module seismicrna.core.mu.scale module seismicrna.core.mu.tests module seismicrna.core.mu.tests.compare_test module seismicrna.core.mu.tests.dim_test module seismicrna.core.mu.tests.frame_test module seismicrna.core.mu.tests.measure_test module seismicrna.core.mu.tests.nan_test module seismicrna.core.mu.tests.scale_test module seismicrna.core.mu.tests.unbias_test module seismicrna.core.mu.unbias module seismicrna.core.ngs module seismicrna.core.ngs.phred module seismicrna.core.ngs.tests module seismicrna.core.ngs.tests.phred_test module seismicrna.core.ngs.xam module seismicrna.core.path module seismicrna.core.rel module seismicrna.core.rel.code module seismicrna.core.rel.pattern module seismicrna.core.rel.tests module seismicrna.core.rel.tests.code_test module seismicrna.core.report module seismicrna.core.rna module seismicrna.core.rna.base module seismicrna.core.rna.convert module seismicrna.core.rna.ct module seismicrna.core.rna.db module seismicrna.core.rna.io module seismicrna.core.rna.pair module seismicrna.core.rna.profile module seismicrna.core.rna.roc module seismicrna.core.rna.state module seismicrna.core.rna.struct module seismicrna.core.rna.tests module seismicrna.core.rna.tests.db_test module seismicrna.core.rna.tests.pair_test module seismicrna.core.run module seismicrna.core.seq module seismicrna.core.seq.fasta module seismicrna.core.seq.refs module seismicrna.core.seq.section module seismicrna.core.seq.tests module seismicrna.core.seq.tests.fasta_test module seismicrna.core.seq.tests.section_test module seismicrna.core.seq.tests.xna_test module seismicrna.core.seq.xna module seismicrna.core.stats module seismicrna.core.task module seismicrna.core.tests module seismicrna.core.tests.array_test module seismicrna.core.tests.header_test module seismicrna.core.tests.stats_test module seismicrna.core.tests.version_test module seismicrna.core.tmp module seismicrna.core.types module seismicrna.core.version module seismicrna.core.write module seismicrna.demult module seismicrna.demult.demultiplex module seismicrna.demult.main module seismicrna.export module seismicrna.export.main module seismicrna.export.meta module seismicrna.export.web module seismicrna.fold module seismicrna.fold.load module seismicrna.fold.main module seismicrna.fold.report module seismicrna.fold.rnastructure module seismicrna.graph module seismicrna.graph.aucroll module seismicrna.graph.base module seismicrna.graph.color module seismicrna.graph.corroll module seismicrna.graph.delprof module seismicrna.graph.giniroll module seismicrna.graph.hist module seismicrna.graph.histpos module seismicrna.graph.histread module seismicrna.graph.histrel module seismicrna.graph.main module seismicrna.graph.onestruct module seismicrna.graph.onetable module seismicrna.graph.profile module seismicrna.graph.rel module seismicrna.graph.roc module seismicrna.graph.roll module seismicrna.graph.scatter module seismicrna.graph.snrroll module seismicrna.graph.statroll module seismicrna.graph.trace module seismicrna.graph.twotable module seismicrna.join module seismicrna.joinbase module seismicrna.joinbase.cluster module seismicrna.joinbase.data module seismicrna.joinbase.report module seismicrna.lists module seismicrna.lists.listpos module seismicrna.lists.lists module seismicrna.main module seismicrna.mask module seismicrna.mask.batch module seismicrna.mask.data module seismicrna.mask.io module seismicrna.mask.main module seismicrna.mask.report module seismicrna.mask.write module seismicrna.pool module seismicrna.pool.data module seismicrna.pool.main module seismicrna.pool.report module seismicrna.relate module seismicrna.relate.aux module seismicrna.relate.aux.cigarop module seismicrna.relate.aux.human module seismicrna.relate.aux.infer module seismicrna.relate.aux.iterread module seismicrna.relate.aux.iterrel module seismicrna.relate.aux.tests module seismicrna.relate.aux.tests.cigarop_test module seismicrna.relate.aux.tests.infer_test module seismicrna.relate.aux.tests.iterrel_test module seismicrna.relate.batch module seismicrna.relate.c module seismicrna.relate.data module seismicrna.relate.io module seismicrna.relate.main module seismicrna.relate.py module seismicrna.relate.py.ambindel module seismicrna.relate.py.cigar module seismicrna.relate.py.encode module seismicrna.relate.py.error module seismicrna.relate.py.relate module seismicrna.relate.py.tests module seismicrna.relate.py.tests.ambindel_test module seismicrna.relate.py.tests.cigar_test module seismicrna.relate.py.tests.encode_test module seismicrna.relate.py.tests.relate_test module seismicrna.relate.report module seismicrna.relate.sam module seismicrna.relate.sim module seismicrna.relate.tests module seismicrna.relate.tests.sim_test module seismicrna.relate.write module seismicrna.renumct module seismicrna.renumct.main module seismicrna.sim module seismicrna.sim.clusts module seismicrna.sim.ends module seismicrna.sim.fastq module seismicrna.sim.fold module seismicrna.sim.main module seismicrna.sim.muts module seismicrna.sim.params module seismicrna.sim.ref module seismicrna.sim.relate module seismicrna.sim.tests module seismicrna.sim.tests.ends_test module seismicrna.sim.total module seismicrna.table module seismicrna.table.base module seismicrna.table.calc module seismicrna.table.load module seismicrna.table.main module seismicrna.table.write module seismicrna.test module seismicrna.test.main module seismicrna.wf module select() (seismicrna.core.header.Header method) sep_strands_bam() (in module seismicrna.align.write) seq (seismicrna.core.rna.base.RNASection property) (seismicrna.graph.base.GraphBase property) (seismicrna.graph.onetable.OneTableGraph property) (seismicrna.graph.twotable.TwoTableGraph property) (seismicrna.relate.py.relate.SamRead attribute) (seismicrna.table.base.PosTable property) seq_pos_to_index() (in module seismicrna.core.seq.section) seq_record (seismicrna.core.rna.base.RNASection property) SeqColorMap (class in seismicrna.graph.color) Sequence_Obj (class in seismicrna.demult.demultiplex) set_config() (in module seismicrna.core.logs) setUp() (seismicrna.align.tests.fqutil_test.TestRunFASTQC method) ShellCommand (class in seismicrna.core.extern.shell) signature (seismicrna.core.header.Header property) (seismicrna.core.header.RelHeader property) sim_pclust() (in module seismicrna.sim.clusts) sim_pclust_ct() (in module seismicrna.sim.clusts) sim_pends() (in module seismicrna.sim.ends) sim_pends_ct() (in module seismicrna.sim.ends) sim_pmut() (in module seismicrna.sim.muts) simulate() (seismicrna.relate.batch.QnamesBatch class method) (seismicrna.relate.batch.RelateBatch class method) simulate_batch() (in module seismicrna.relate.sim) simulate_batches() (in module seismicrna.relate.sim) simulate_cluster() (in module seismicrna.relate.sim) simulate_muts() (in module seismicrna.core.batch.muts) simulate_params() (in module seismicrna.core.mu.tests.unbias_test) simulate_reads() (in module seismicrna.core.mu.tests.unbias_test) simulate_relate() (in module seismicrna.relate.sim) simulate_segment_ends() (in module seismicrna.core.batch.ends) size (seismicrna.core.header.Header property) (seismicrna.core.seq.section.Section property) sort_replicate_runs() (in module seismicrna.cluster.compare) sort_segment_ends() (in module seismicrna.core.batch.ends) sort_xam_cmd() (in module seismicrna.core.ngs.xam) split_fastq() (seismicrna.demult.demultiplex.super_fastq method) stamp() (seismicrna.relate.py.ambindel.Insertion method) standardize() (in module seismicrna.core.mu.scale) stat_func() (seismicrna.graph.giniroll.RollingGiniGraph class method) (seismicrna.graph.snrroll.RollingSNRGraph class method) (seismicrna.graph.statroll.RollingStatGraph class method) step_del_pos() (seismicrna.relate.py.ambindel.Indel method) stochastic_round() (in module seismicrna.core.array) struct_sect (seismicrna.graph.onestruct.StructOneTableGraph property) StructOneTableGraph (class in seismicrna.graph.onestruct) StructOneTableRunner (class in seismicrna.graph.onestruct) StructOneTableWriter (class in seismicrna.graph.onestruct) subsection() (seismicrna.core.rna.base.RNASection method) (seismicrna.core.seq.section.Section method) super_fastq (class in seismicrna.demult.demultiplex) super_write_fastqs() (seismicrna.demult.demultiplex.super_fastq method) sweep() (seismicrna.relate.py.ambindel.Deletion method) (seismicrna.relate.py.ambindel.Indel method) (seismicrna.relate.py.ambindel.Insertion method) sweep_indels() (in module seismicrna.relate.py.ambindel)

T

t (seismicrna.core.rel.pattern.HalfRelPattern attribute) t_or_u() (seismicrna.core.seq.xna.XNA class method) Table (class in seismicrna.table.base) table (seismicrna.graph.onetable.OneTableWriter property) table1 (seismicrna.graph.twotable.TwoTableWriter property) table2 (seismicrna.graph.twotable.TwoTableWriter property) table_per_clust (seismicrna.table.calc.ClustTabulator property) table_per_pos (seismicrna.table.calc.PartialTabulator property) (seismicrna.table.calc.Tabulator property) table_per_read (seismicrna.table.calc.Tabulator property) table_to_dict() (in module seismicrna.core.rna.pair) table_to_pairs() (in module seismicrna.core.rna.pair) TableLoader (class in seismicrna.table.load) TableWriter (class in seismicrna.table.write) tabulate_loader() (in module seismicrna.table.calc) Tabulator (class in seismicrna.table.calc) TallDataset (class in seismicrna.core.data) TallMutsDataset (class in seismicrna.core.data) Task (class in seismicrna.core.task) tearDown() (seismicrna.align.tests.fqutil_test.TestRunFASTQC method) test_0() (seismicrna.core.mu.tests.unbias_test.TestFindSplitPositions method) test_0_clusters() (seismicrna.cluster.tests.compare_test.TestAssignClusterings method) test_0_positions() (seismicrna.cluster.tests.compare_test.TestAssignClusterings method) (seismicrna.core.batch.tests.count_test.TestCalcCoverage method) test_0_positions_weighted() (seismicrna.core.batch.tests.count_test.TestCalcCoverage method) test_0_reads() (seismicrna.core.batch.tests.count_test.TestCalcUniqReadWeights method) test_0_segments() (seismicrna.core.batch.tests.ends_test.TestCountReadsSegments method) test_0d() (seismicrna.core.tests.array_test.TestFindDims method) test_0d_1dim() (seismicrna.core.tests.array_test.TestFindDims method) test_0d_none() (seismicrna.core.tests.array_test.TestFindDims method) test_0d_nonzero() (seismicrna.core.tests.array_test.TestFindDims method) test_0d_nonzero_extra() (seismicrna.core.tests.array_test.TestFindDims method) test_0x0() (seismicrna.core.mu.tests.unbias_test.TestSlicePEnds method) (seismicrna.core.mu.tests.unbias_test.TestTriuNorm method) test_0x0x1() (seismicrna.core.mu.tests.unbias_test.TestTriuNorm method) test_1_cluster() (seismicrna.cluster.tests.compare_test.TestAssignClusterings method) test_1_dim() (seismicrna.core.mu.tests.unbias_test.TestPublicCalcPNoCloseGivenEnds method) test_1_position() (seismicrna.core.batch.tests.count_test.TestCalcCoverage method) test_1_read() (seismicrna.core.batch.tests.count_test.TestCalcUniqReadWeights method) test_1_segment() (seismicrna.core.batch.tests.count_test.TestCalcCoverage method) (seismicrna.core.batch.tests.ends_test.TestFindContiguousReads method) (seismicrna.core.batch.tests.ends_test.TestFindReadEnd3s method) (seismicrna.core.batch.tests.ends_test.TestFindReadEnd5s method) (seismicrna.core.batch.tests.ends_test.TestSortSegmentEnds method) test_1_segment_all_covered() (seismicrna.core.batch.tests.ends_test.TestCheckNoCoverageReads method) test_1_segment_none_covered() (seismicrna.core.batch.tests.ends_test.TestCheckNoCoverageReads method) test_1_segment_redundant() (seismicrna.core.batch.tests.count_test.TestCalcCoverage method) test_1_segment_redundant_weighted() (seismicrna.core.batch.tests.count_test.TestCalcCoverage method) test_1_segment_weighted() (seismicrna.core.batch.tests.count_test.TestCalcCoverage method) test_1_series_size_1_min_0_excl_nan() (seismicrna.core.seq.tests.section_test.TestGetWindows method) test_1_series_size_1_min_0_incl_nan() (seismicrna.core.seq.tests.section_test.TestGetWindows method) test_1_series_size_1_min_1_excl_nan() (seismicrna.core.seq.tests.section_test.TestGetWindows method) test_1_series_size_1_min_1_incl_nan() (seismicrna.core.seq.tests.section_test.TestGetWindows method) test_1_series_size_2_min_1_excl_nan() (seismicrna.core.seq.tests.section_test.TestGetWindows method) test_1_series_size_2_min_1_incl_nan() (seismicrna.core.seq.tests.section_test.TestGetWindows method) test_1_series_size_2_min_2_excl_nan() (seismicrna.core.seq.tests.section_test.TestGetWindows method) test_1_series_size_2_min_2_incl_nan() (seismicrna.core.seq.tests.section_test.TestGetWindows method) test_1d() (seismicrna.core.mu.tests.measure_test.TestCalcSignalNoise method) (seismicrna.core.tests.array_test.TestFindDims method) (seismicrna.core.tests.array_test.TestGetLength method) test_1d_0dim_none() (seismicrna.core.tests.array_test.TestFindDims method) test_1d_1d_crossed() (seismicrna.core.tests.array_test.TestFindDims method) test_1d_1d_separate() (seismicrna.core.tests.array_test.TestFindDims method) test_1d_1dim_none() (seismicrna.core.tests.array_test.TestFindDims method) test_1d_2d_congruent() (seismicrna.core.tests.array_test.TestFindDims method) test_1d_2d_crossed() (seismicrna.core.tests.array_test.TestFindDims method) test_1d_2dim() (seismicrna.core.tests.array_test.TestFindDims method) test_1d_2dim_none() (seismicrna.core.tests.array_test.TestFindDims method) test_1d_nonzero() (seismicrna.core.tests.array_test.TestFindDims method) test_1pos() (seismicrna.cluster.tests.em_test.TestExpectation method) test_1pos_2clusters() (seismicrna.cluster.tests.em_test.TestExpectation method) test_1x1() (seismicrna.core.mu.tests.unbias_test.TestTriuDiv method) (seismicrna.core.mu.tests.unbias_test.TestTriuDot method) (seismicrna.core.mu.tests.unbias_test.TestTriuNorm method) (seismicrna.core.mu.tests.unbias_test.TestTriuSum method) test_1x1x1() (seismicrna.core.mu.tests.unbias_test.TestTriuDiv method) (seismicrna.core.mu.tests.unbias_test.TestTriuDot method) (seismicrna.core.mu.tests.unbias_test.TestTriuNorm method) (seismicrna.core.mu.tests.unbias_test.TestTriuSum method) test_1x1x2() (seismicrna.core.mu.tests.unbias_test.TestTriuCumSum method) (seismicrna.core.mu.tests.unbias_test.TestTriuNorm method) (seismicrna.core.mu.tests.unbias_test.TestTriuSum method) test_2_dim() (seismicrna.core.mu.tests.unbias_test.TestPublicCalcPNoCloseGivenEnds method) test_2_reads_1_uniq() (seismicrna.core.batch.tests.count_test.TestCalcUniqReadWeights method) test_2_reads_2_uniq() (seismicrna.core.batch.tests.count_test.TestCalcUniqReadWeights method) test_2_segments_all_covered() (seismicrna.core.batch.tests.ends_test.TestCheckNoCoverageReads method) test_2_segments_half_covered() (seismicrna.core.batch.tests.ends_test.TestCheckNoCoverageReads method) test_2_segments_mask() (seismicrna.core.batch.tests.count_test.TestCalcCoverage method) (seismicrna.core.batch.tests.ends_test.TestFindContiguousReads method) (seismicrna.core.batch.tests.ends_test.TestFindReadEnd3s method) (seismicrna.core.batch.tests.ends_test.TestFindReadEnd5s method) (seismicrna.core.batch.tests.ends_test.TestSortSegmentEnds method) test_2_segments_nomask() (seismicrna.core.batch.tests.count_test.TestCalcCoverage method) (seismicrna.core.batch.tests.ends_test.TestFindContiguousReads method) (seismicrna.core.batch.tests.ends_test.TestFindReadEnd3s method) (seismicrna.core.batch.tests.ends_test.TestFindReadEnd5s method) (seismicrna.core.batch.tests.ends_test.TestSortSegmentEnds method) test_2_segments_none_covered() (seismicrna.core.batch.tests.ends_test.TestCheckNoCoverageReads method) test_2_segments_unmask() (seismicrna.core.batch.tests.ends_test.TestSortSegmentEnds method) test_2_series_size_1_min_0_excl_nan() (seismicrna.core.seq.tests.section_test.TestGetWindows method) test_2_series_size_1_min_0_incl_nan() (seismicrna.core.seq.tests.section_test.TestGetWindows method) test_2_series_size_1_min_1_excl_nan() (seismicrna.core.seq.tests.section_test.TestGetWindows method) test_2_series_size_1_min_1_incl_nan() (seismicrna.core.seq.tests.section_test.TestGetWindows method) test_2_series_size_2_min_0_excl_nan() (seismicrna.core.seq.tests.section_test.TestGetWindows method) test_2_series_size_2_min_0_incl_nan() (seismicrna.core.seq.tests.section_test.TestGetWindows method) test_2_series_size_2_min_1_excl_nan() (seismicrna.core.seq.tests.section_test.TestGetWindows method) test_2_series_size_2_min_1_incl_nan() (seismicrna.core.seq.tests.section_test.TestGetWindows method) test_2_series_size_2_min_2_excl_nan() (seismicrna.core.seq.tests.section_test.TestGetWindows method) test_2_series_size_2_min_2_incl_nan() (seismicrna.core.seq.tests.section_test.TestGetWindows method) test_2d() (seismicrna.core.mu.tests.measure_test.TestCalcSignalNoise method) (seismicrna.core.mu.tests.unbias_test.TestCalcRectangularSum method) (seismicrna.core.mu.tests.unbias_test.TestTriuLog method) (seismicrna.core.tests.array_test.TestFindDims method) test_2d_1dim_none() (seismicrna.core.tests.array_test.TestFindDims method) test_2d_2d_congruent() (seismicrna.core.tests.array_test.TestFindDims method) test_2d_2d_crossed() (seismicrna.core.tests.array_test.TestFindDims method) test_2d_nonzero() (seismicrna.core.tests.array_test.TestFindDims method) test_2pos_gap0() (seismicrna.cluster.tests.em_test.TestExpectation method) test_2pos_gap0_2clusters() (seismicrna.cluster.tests.em_test.TestExpectation method) test_2pos_gap1() (seismicrna.cluster.tests.em_test.TestExpectation method) test_2pos_masked0() (seismicrna.cluster.tests.em_test.TestExpectation method) test_2pos_masked1() (seismicrna.cluster.tests.em_test.TestExpectation method) test_2x2() (seismicrna.core.mu.tests.unbias_test.TestTriuCumSum method) (seismicrna.core.mu.tests.unbias_test.TestTriuDiv method) (seismicrna.core.mu.tests.unbias_test.TestTriuDot method) (seismicrna.core.mu.tests.unbias_test.TestTriuNorm method) (seismicrna.core.mu.tests.unbias_test.TestTriuSum method) test_2x2_zero() (seismicrna.core.mu.tests.unbias_test.TestTriuNorm method) test_2x2x1() (seismicrna.core.mu.tests.unbias_test.TestTriuCumSum method) (seismicrna.core.mu.tests.unbias_test.TestTriuNorm method) (seismicrna.core.mu.tests.unbias_test.TestTriuSum method) test_2x2x2() (seismicrna.core.mu.tests.unbias_test.TestTriuCumSum method) (seismicrna.core.mu.tests.unbias_test.TestTriuDiv method) (seismicrna.core.mu.tests.unbias_test.TestTriuDot method) (seismicrna.core.mu.tests.unbias_test.TestTriuNorm method) (seismicrna.core.mu.tests.unbias_test.TestTriuSum method) test_2x2x2_zero() (seismicrna.core.mu.tests.unbias_test.TestTriuNorm method) test_2x2x2x2() (seismicrna.core.mu.tests.unbias_test.TestTriuNorm method) (seismicrna.core.mu.tests.unbias_test.TestTriuSum method) test_2x2x2x2_zero() (seismicrna.core.mu.tests.unbias_test.TestTriuNorm method) test_3d() (seismicrna.core.mu.tests.unbias_test.TestCalcRectangularSum method) (seismicrna.core.mu.tests.unbias_test.TestTriuLog method) test_3x3() (seismicrna.core.mu.tests.unbias_test.TestTriuCumSum method) test_a() (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsQ53 method) test_aa() (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsQ53 method) test_aaaa_0ins() (seismicrna.relate.py.tests.relate_test.TestFindRelsLine method) test_aaaaaa_0ins() (seismicrna.relate.py.tests.relate_test.TestFindRelsLine method) test_aacc_1ins() (seismicrna.relate.py.tests.relate_test.TestFindRelsLine method) test_abstract() (seismicrna.core.tests.header_test.TestHeader method) test_abstract_base_class() (seismicrna.core.seq.tests.xna_test.TestXNA method) test_acgt_1ins() (seismicrna.relate.py.tests.relate_test.TestFindRelsLine method) test_add_mask() (seismicrna.core.seq.tests.section_test.TestSectionAddMask method) test_add_mask_invalid() (seismicrna.core.seq.tests.section_test.TestSectionAddMask method) test_add_mask_invert() (seismicrna.core.seq.tests.section_test.TestSectionAddMask method) test_add_overlapping_masks() (seismicrna.core.seq.tests.section_test.TestSectionAddMask method) test_add_unordered_mask() (seismicrna.core.seq.tests.section_test.TestSectionAddMask method) test_agg() (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsQ53 method) test_all() (seismicrna.core.tests.header_test.TestMakeHeader method) test_all_0() (seismicrna.core.mu.tests.unbias_test.TestTriuCumSum method) test_all_1() (seismicrna.core.mu.tests.unbias_test.TestTriuCumSum method) test_all_equal_1d() (seismicrna.core.mu.tests.measure_test.TestCalcGini method) test_all_equal_2d() (seismicrna.core.mu.tests.measure_test.TestCalcGini method) test_all_false() (seismicrna.core.tests.array_test.TestFindTrueDists method) test_all_match() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) test_all_match_n() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) test_all_matches() (seismicrna.relate.py.tests.relate_test.TestFindRelsLine method) test_all_true() (seismicrna.core.tests.array_test.TestFindTrueDists method) test_all_zero() (seismicrna.core.mu.tests.unbias_test.TestTriuSum method) test_all_zero_1d() (seismicrna.core.mu.tests.measure_test.TestCalcGini method) test_all_zero_2d() (seismicrna.core.mu.tests.measure_test.TestCalcGini method) test_alph() (seismicrna.core.seq.tests.xna_test.TestDNA method) (seismicrna.core.seq.tests.xna_test.TestRNA method) test_ambig_delet_low_qual() (seismicrna.relate.py.tests.relate_test.TestFindRelsLine method) test_array() (seismicrna.core.mu.tests.nan_test.TestAutoRemoveNaN method) (seismicrna.core.mu.tests.nan_test.TestAutoRemovesNaN method) test_array0d() (seismicrna.core.mu.tests.compare_test.TestCalcCoeffDeterm method) (seismicrna.core.mu.tests.compare_test.TestCalcNRMSD method) (seismicrna.core.mu.tests.compare_test.TestCalcPearson method) (seismicrna.core.mu.tests.compare_test.TestCalcSpearman method) (seismicrna.core.mu.tests.dim_test.TestCountPos method) (seismicrna.core.mu.tests.nan_test.TestAnyNaN method) (seismicrna.core.mu.tests.scale_test.TestCalcQuantile method) (seismicrna.core.mu.tests.scale_test.TestCalcRanks method) (seismicrna.core.mu.tests.scale_test.TestCalcRMS method) (seismicrna.core.mu.tests.scale_test.TestNormalize method) (seismicrna.core.mu.tests.scale_test.TestStandardize method) test_array1d() (seismicrna.core.mu.tests.compare_test.TestCalcCoeffDeterm method) (seismicrna.core.mu.tests.compare_test.TestCalcPearson method) (seismicrna.core.mu.tests.compare_test.TestCalcSpearman method) (seismicrna.core.mu.tests.dim_test.TestCountPos method) (seismicrna.core.mu.tests.dim_test.TestCountsPos method) (seismicrna.core.mu.tests.nan_test.TestAnyNaN method) (seismicrna.core.mu.tests.nan_test.TestNoNaN method) (seismicrna.core.mu.tests.nan_test.TestRemoveNaNs method) (seismicrna.core.mu.tests.nan_test.TestRemovesNaNs method) (seismicrna.core.mu.tests.scale_test.TestCalcQuantile method) (seismicrna.core.mu.tests.scale_test.TestCalcRanks method) (seismicrna.core.mu.tests.scale_test.TestCalcRMS method) (seismicrna.core.mu.tests.scale_test.TestNormalize method) (seismicrna.core.mu.tests.scale_test.TestStandardize method) test_array1d_all_nan() (seismicrna.core.mu.tests.scale_test.TestCalcQuantile method) test_array1d_allzero() (seismicrna.core.mu.tests.compare_test.TestCalcNRMSD method) test_array1d_empty() (seismicrna.core.mu.tests.scale_test.TestCalcQuantile method) test_array1d_examples() (seismicrna.core.mu.tests.compare_test.TestCalcNRMSD method) test_array1d_extremes() (seismicrna.core.mu.tests.compare_test.TestCalcNRMSD method) test_array1d_nan() (seismicrna.core.mu.tests.compare_test.TestCalcSpearman method) (seismicrna.core.mu.tests.scale_test.TestCalcRMS method) (seismicrna.core.mu.tests.scale_test.TestNormalize method) test_array1d_some_nan() (seismicrna.core.mu.tests.scale_test.TestCalcQuantile method) test_array2d() (seismicrna.core.mu.tests.compare_test.TestCalcNRMSD method) (seismicrna.core.mu.tests.compare_test.TestCalcPearson method) (seismicrna.core.mu.tests.compare_test.TestCalcSpearman method) (seismicrna.core.mu.tests.dim_test.TestCountPos method) (seismicrna.core.mu.tests.nan_test.TestAnyNaN method) (seismicrna.core.mu.tests.nan_test.TestNoNaN method) (seismicrna.core.mu.tests.nan_test.TestRemoveNaNs method) (seismicrna.core.mu.tests.nan_test.TestRemovesNaNs method) (seismicrna.core.mu.tests.scale_test.TestCalcQuantile method) (seismicrna.core.mu.tests.scale_test.TestCalcRanks method) (seismicrna.core.mu.tests.scale_test.TestCalcRMS method) (seismicrna.core.mu.tests.scale_test.TestNormalize method) (seismicrna.core.mu.tests.scale_test.TestStandardize method) test_array2d_one_col_nan() (seismicrna.core.mu.tests.scale_test.TestCalcQuantile method) test_array2d_one_row_nan() (seismicrna.core.mu.tests.scale_test.TestCalcQuantile method) test_array3d() (seismicrna.core.mu.tests.nan_test.TestAnyNaN method) (seismicrna.core.mu.tests.scale_test.TestCalcRanks method) test_array_array() (seismicrna.core.mu.tests.frame_test.TestReframeLike method) test_array_dataframe() (seismicrna.core.mu.tests.frame_test.TestReframeLike method) test_array_index() (seismicrna.core.mu.tests.frame_test.TestReframe method) test_array_index_index() (seismicrna.core.mu.tests.frame_test.TestReframe method) test_array_ints() (seismicrna.core.mu.tests.frame_test.TestReframe method) test_array_none() (seismicrna.core.mu.tests.frame_test.TestReframe method) test_array_series() (seismicrna.core.mu.tests.frame_test.TestReframeLike method) test_array_series_dataframe() (seismicrna.core.mu.tests.nan_test.TestRemovesNaNs method) test_array_series_dataframe_mismatched() (seismicrna.core.mu.tests.nan_test.TestRemovesNaNs method) test_arrays() (seismicrna.core.mu.tests.scale_test.TestWinsorize method) test_average_prefix() (seismicrna.core.tests.header_test.TestConstants method) test_base_name() (seismicrna.core.seq.tests.section_test.TestConstants method) test_blank() (seismicrna.core.seq.tests.fasta_test.TestValidFastaSeqname method) test_bool() (seismicrna.core.seq.tests.xna_test.TestDNA method) (seismicrna.core.seq.tests.xna_test.TestRNA method) test_both_blank() (seismicrna.relate.py.tests.relate_test.TestMergeMates method) test_both_reads() (seismicrna.relate.py.tests.relate_test.TestMergeMates method) test_c() (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsQ53 method) test_calc_inverse() (seismicrna.core.tests.array_test.TestCalcInverse method) test_calc_inverse_fill_fwd() (seismicrna.core.tests.array_test.TestCalcInverse method) test_calc_inverse_fill_fwd_max() (seismicrna.core.tests.array_test.TestCalcInverse method) test_calc_inverse_fill_fwd_max_default() (seismicrna.core.tests.array_test.TestCalcInverse method) test_calc_inverse_fill_rev() (seismicrna.core.tests.array_test.TestCalcInverse method) test_calc_inverse_fill_rev_max() (seismicrna.core.tests.array_test.TestCalcInverse method) test_calc_inverse_fill_rev_max_default() (seismicrna.core.tests.array_test.TestCalcInverse method) test_calc_inverse_max() (seismicrna.core.tests.array_test.TestCalcInverse method) test_calc_p_ends_given_observed() (seismicrna.core.mu.tests.unbias_test.TestCalcPEndsObserved method) test_cigar_align_valid() (seismicrna.relate.py.tests.cigar_test.TestParseCigar method) test_cigar_init_invalid() (seismicrna.relate.aux.tests.cigarop_test.TestCigarOp method) test_cigar_init_valid() (seismicrna.relate.aux.tests.cigarop_test.TestCigarOp method) test_cigar_lengthen() (seismicrna.relate.aux.tests.cigarop_test.TestCigarOp method) test_cigar_m_aln_valid() (seismicrna.relate.aux.tests.cigarop_test.TestFindCigarOpPos method) test_cigar_m_del_valid() (seismicrna.relate.aux.tests.cigarop_test.TestFindCigarOpPos method) test_cigar_m_ins_valid() (seismicrna.relate.aux.tests.cigarop_test.TestFindCigarOpPos method) test_cigar_m_mat_valid() (seismicrna.relate.aux.tests.cigarop_test.TestFindCigarOpPos method) test_cigar_m_scl_valid() (seismicrna.relate.aux.tests.cigarop_test.TestFindCigarOpPos method) test_cigar_m_sub_valid() (seismicrna.relate.aux.tests.cigarop_test.TestFindCigarOpPos method) test_cigar_match_subst_valid() (seismicrna.relate.aux.tests.cigarop_test.TestCountCigarMuts method) (seismicrna.relate.py.tests.cigar_test.TestParseCigar method) test_cigar_str() (seismicrna.relate.aux.tests.cigarop_test.TestCigarOp method) test_cigar_xeq_aln_valid() (seismicrna.relate.aux.tests.cigarop_test.TestFindCigarOpPos method) test_cigar_xeq_del_valid() (seismicrna.relate.aux.tests.cigarop_test.TestFindCigarOpPos method) test_cigar_xeq_ins_valid() (seismicrna.relate.aux.tests.cigarop_test.TestFindCigarOpPos method) test_cigar_xeq_mat_valid() (seismicrna.relate.aux.tests.cigarop_test.TestFindCigarOpPos method) test_cigar_xeq_scl_valid() (seismicrna.relate.aux.tests.cigarop_test.TestFindCigarOpPos method) test_cigar_xeq_sub_valid() (seismicrna.relate.aux.tests.cigarop_test.TestFindCigarOpPos method) test_clust() (seismicrna.core.tests.header_test.TestParseHeader method) test_clust_name() (seismicrna.core.tests.header_test.TestConstants method) test_cluster_prefix() (seismicrna.core.tests.header_test.TestConstants method) test_clustered() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_clusters() (seismicrna.core.mu.tests.unbias_test.TestCalcPMutGivenSpanNoClose method) (seismicrna.core.mu.tests.unbias_test.TestPrivateCalcPNoCloseGivenEnds method) test_clustheaders() (seismicrna.core.tests.header_test.TestEqualHeaders method) test_clusts() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_comps() (seismicrna.core.mu.tests.compare_test.TestGetComp method) test_conflicting_pair_1() (seismicrna.core.rna.tests.pair_test.TestPairsToDict method) (seismicrna.core.rna.tests.pair_test.TestPairsToTable method) test_conflicting_pair_2() (seismicrna.core.rna.tests.pair_test.TestPairsToDict method) (seismicrna.core.rna.tests.pair_test.TestPairsToTable method) test_contains() (seismicrna.core.seq.tests.xna_test.TestDNA method) test_contiguous() (seismicrna.core.mu.tests.compare_test.TestCompareWindows method) test_copy() (seismicrna.core.seq.tests.section_test.TestSectionCopy method) test_custom_1() (seismicrna.core.tests.array_test.TestFindTrueDists method) test_custom_2() (seismicrna.core.tests.array_test.TestFindTrueDists method) test_dangling_closer() (seismicrna.core.rna.tests.db_test.TestParseDbStructure method) test_dangling_opener() (seismicrna.core.rna.tests.db_test.TestParseDbStructure method) test_dataframe() (seismicrna.core.mu.tests.compare_test.TestCalcCoeffDeterm method) (seismicrna.core.mu.tests.compare_test.TestCalcNRMSD method) (seismicrna.core.mu.tests.compare_test.TestCalcPearson method) (seismicrna.core.mu.tests.compare_test.TestCalcSpearman method) (seismicrna.core.mu.tests.dim_test.TestCountPos method) (seismicrna.core.mu.tests.dim_test.TestCountsPos method) (seismicrna.core.mu.tests.frame_test.TestReframe method) (seismicrna.core.mu.tests.nan_test.TestAnyNaN method) (seismicrna.core.mu.tests.nan_test.TestNoNaN method) (seismicrna.core.mu.tests.nan_test.TestRemoveNaNs method) (seismicrna.core.mu.tests.nan_test.TestRemovesNaNs method) (seismicrna.core.mu.tests.scale_test.TestCalcQuantile method) (seismicrna.core.mu.tests.scale_test.TestCalcRanks method) (seismicrna.core.mu.tests.scale_test.TestCalcRMS method) (seismicrna.core.mu.tests.scale_test.TestNormalize method) (seismicrna.core.mu.tests.scale_test.TestStandardize method) (seismicrna.core.mu.tests.scale_test.TestWinsorize method) test_dataframe_array() (seismicrna.core.mu.tests.frame_test.TestReframeLike method) test_dataframe_dataframe() (seismicrna.core.mu.tests.frame_test.TestReframeLike method) test_decode() (seismicrna.core.ngs.tests.phred_test.TestDecode method) test_deep_pairs() (seismicrna.core.rna.tests.db_test.TestFormatDbStructure method) (seismicrna.core.rna.tests.db_test.TestParseDbStructure method) test_delete_invalid() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) test_delete_valid() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) test_derived_codes() (seismicrna.core.rel.tests.code_test.TestConstants method) test_dict_str_dna_rna() (seismicrna.core.seq.tests.xna_test.TestXNA method) test_diff_end3() (seismicrna.core.seq.tests.section_test.TestSectionEqual method) test_diff_end5() (seismicrna.core.seq.tests.section_test.TestSectionEqual method) test_diff_full() (seismicrna.core.seq.tests.section_test.TestSectionEqual method) test_diff_lengths() (seismicrna.core.tests.array_test.TestEnsureSameLength method) test_diff_mask_name() (seismicrna.core.seq.tests.section_test.TestSectionEqual method) test_diff_mask_positions() (seismicrna.core.seq.tests.section_test.TestSectionEqual method) test_diff_name() (seismicrna.core.seq.tests.section_test.TestSectionEqual method) test_diff_ref() (seismicrna.core.seq.tests.section_test.TestSectionEqual method) test_diff_refs() (seismicrna.core.seq.tests.section_test.TestIntersect method) (seismicrna.core.seq.tests.section_test.TestUnite method) test_diff_seq() (seismicrna.core.seq.tests.section_test.TestSectionEqual method) test_diff_seq5() (seismicrna.core.seq.tests.section_test.TestSectionEqual method) test_diff_seqs() (seismicrna.core.seq.tests.section_test.TestIntersect method) (seismicrna.core.seq.tests.section_test.TestUnite method) test_different_types() (seismicrna.core.tests.header_test.TestEqualHeaders method) test_distributed_1d() (seismicrna.core.mu.tests.measure_test.TestCalcGini method) test_drop_array() (seismicrna.core.mu.tests.frame_test.TestReframeLike method) test_drop_dataframe() (seismicrna.core.mu.tests.frame_test.TestReframeLike method) test_drop_series() (seismicrna.core.mu.tests.frame_test.TestReframeLike method) test_duplicate_name() (seismicrna.core.seq.tests.fasta_test.TestParseFasta method) test_empty() (seismicrna.core.mu.tests.dim_test.TestCountsPosConsensus method) (seismicrna.core.mu.tests.nan_test.TestRemovesNaNs method) (seismicrna.core.rna.tests.pair_test.TestDictToPairs method) (seismicrna.core.rna.tests.pair_test.TestDictToTable method) (seismicrna.core.rna.tests.pair_test.TestPairsToDict method) (seismicrna.core.rna.tests.pair_test.TestTableToDict method) (seismicrna.core.rna.tests.pair_test.TestTableToPairs method) (seismicrna.core.seq.tests.section_test.TestGetWindows method) (seismicrna.core.tests.array_test.TestCalcInverse method) (seismicrna.core.tests.array_test.TestFindDims method) (seismicrna.relate.py.tests.relate_test.TestMergeMates method) test_empty_1d() (seismicrna.core.mu.tests.measure_test.TestCalcGini method) (seismicrna.core.mu.tests.measure_test.TestCalcSignalNoise method) test_empty_invalid() (seismicrna.core.seq.tests.section_test.TestIntersect method) (seismicrna.core.seq.tests.section_test.TestUnite method) test_empty_max() (seismicrna.core.tests.array_test.TestCalcInverse method) test_encode() (seismicrna.core.ngs.tests.phred_test.TestEncode method) test_encode_match_hi_qual() (seismicrna.relate.py.tests.encode_test.TestEncodeMatch method) test_encode_match_lo_qual() (seismicrna.relate.py.tests.encode_test.TestEncodeMatch method) test_encode_relate_hi_qual() (seismicrna.relate.py.tests.encode_test.TestEncodeRelate method) test_encode_relate_lo_qual() (seismicrna.relate.py.tests.encode_test.TestEncodeRelate method) test_equal() (seismicrna.core.mu.tests.dim_test.TestCountsPosConsensus method) (seismicrna.core.mu.tests.unbias_test.TestTriuAllClose method) test_equal_dna_dna() (seismicrna.core.seq.tests.xna_test.TestXNA method) test_equal_full() (seismicrna.core.seq.tests.section_test.TestSectionEqual method) test_equal_mask() (seismicrna.core.seq.tests.section_test.TestSectionEqual method) test_equal_part() (seismicrna.core.seq.tests.section_test.TestSectionEqual method) test_equal_rna_rna() (seismicrna.core.seq.tests.xna_test.TestXNA method) test_excess_pseudoknot() (seismicrna.core.rna.tests.db_test.TestFormatDbStructure method) test_explicit_sum() (seismicrna.core.mu.tests.unbias_test.TestTriuCumSum method) test_extra_index_names() (seismicrna.core.tests.header_test.TestParseHeader method) test_extra_values() (seismicrna.core.tests.header_test.TestParseHeader method) test_find_gu() (seismicrna.core.seq.tests.section_test.TestSectionMaskGU method) test_find_polya() (seismicrna.core.seq.tests.section_test.TestSectionMaskPolyA method) test_float_array() (seismicrna.core.mu.tests.frame_test.TestReframeLike method) test_float_clust() (seismicrna.core.tests.header_test.TestValidateOrderClust method) test_float_dataframe() (seismicrna.core.mu.tests.frame_test.TestReframeLike method) test_float_float() (seismicrna.core.mu.tests.frame_test.TestReframeLike method) test_float_index() (seismicrna.core.mu.tests.frame_test.TestReframe method) test_float_index_index() (seismicrna.core.mu.tests.frame_test.TestReframe method) test_float_index_index_index() (seismicrna.core.mu.tests.frame_test.TestReframe method) test_float_index_index_int() (seismicrna.core.mu.tests.frame_test.TestReframe method) test_float_index_int() (seismicrna.core.mu.tests.frame_test.TestReframe method) test_float_int_index() (seismicrna.core.mu.tests.frame_test.TestReframe method) test_float_ints() (seismicrna.core.mu.tests.frame_test.TestReframe method) test_float_none() (seismicrna.core.mu.tests.frame_test.TestReframe method) test_float_order() (seismicrna.core.tests.header_test.TestValidateOrderClust method) test_float_series() (seismicrna.core.mu.tests.frame_test.TestReframeLike method) test_format_default() (seismicrna.core.tests.version_test.TestFormatVersion method) test_format_fasta_name_line() (seismicrna.core.seq.tests.fasta_test.TestFormat method) test_format_fasta_record() (seismicrna.core.seq.tests.fasta_test.TestFormat method) test_format_fasta_seq_lines() (seismicrna.core.seq.tests.fasta_test.TestFormat method) test_format_notag() (seismicrna.core.tests.version_test.TestFormatVersion method) test_format_prtag() (seismicrna.core.tests.version_test.TestFormatVersion method) test_fq (seismicrna.align.tests.fqutil_test.TestRunFASTQC attribute) test_fq1 (seismicrna.align.tests.fqutil_test.TestRunFASTQC attribute) test_fq2 (seismicrna.align.tests.fqutil_test.TestRunFASTQC attribute) test_full() (seismicrna.core.seq.tests.section_test.TestSectionInit method) test_full_blank_name() (seismicrna.core.seq.tests.section_test.TestSectionInit method) test_full_end3() (seismicrna.core.seq.tests.section_test.TestSectionInit method) test_full_end5() (seismicrna.core.seq.tests.section_test.TestSectionInit method) test_full_given_name() (seismicrna.core.seq.tests.section_test.TestSectionInit method) test_full_lengths() (seismicrna.core.seq.tests.section_test.TestSectionLength method) test_full_name() (seismicrna.core.seq.tests.section_test.TestConstants method) test_full_reads_no_muts() (seismicrna.core.batch.tests.muts_test.TestCalcMutsMatrix method) test_full_reads_no_muts_some_masked() (seismicrna.core.batch.tests.muts_test.TestCalcMutsMatrix method) test_full_section_full_length_sub() (seismicrna.core.seq.tests.section_test.TestSubsection method) test_full_section_full_sub() (seismicrna.core.seq.tests.section_test.TestSubsection method) test_full_section_full_sub_end3() (seismicrna.core.seq.tests.section_test.TestSubsection method) test_full_section_full_sub_end5() (seismicrna.core.seq.tests.section_test.TestSubsection method) test_full_section_full_sub_name() (seismicrna.core.seq.tests.section_test.TestSubsection method) test_g() (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsQ53 method) test_gap0() (seismicrna.core.mu.tests.unbias_test.TestFindSplitPositions method) test_gap1_single_end3() (seismicrna.core.mu.tests.unbias_test.TestFindSplitPositions method) test_gap1_single_end5() (seismicrna.core.mu.tests.unbias_test.TestFindSplitPositions method) test_gap1_split0_quadruple() (seismicrna.core.mu.tests.unbias_test.TestFindSplitPositions method) test_gap1_split1_double() (seismicrna.core.mu.tests.unbias_test.TestFindSplitPositions method) test_gap1_split1_single_mid() (seismicrna.core.mu.tests.unbias_test.TestFindSplitPositions method) test_gap1_split1_triple() (seismicrna.core.mu.tests.unbias_test.TestFindSplitPositions method) test_gap1_split2() (seismicrna.core.mu.tests.unbias_test.TestFindSplitPositions method) test_gap2_single_end3() (seismicrna.core.mu.tests.unbias_test.TestFindSplitPositions method) test_gap2_single_end5() (seismicrna.core.mu.tests.unbias_test.TestFindSplitPositions method) test_gap2_split0() (seismicrna.core.mu.tests.unbias_test.TestFindSplitPositions method) test_gap2_split1() (seismicrna.core.mu.tests.unbias_test.TestFindSplitPositions method) test_gap3_single_end3() (seismicrna.core.mu.tests.unbias_test.TestFindSplitPositions method) test_gap3_single_end5() (seismicrna.core.mu.tests.unbias_test.TestFindSplitPositions method) test_gap4_split0() (seismicrna.core.mu.tests.unbias_test.TestFindSplitPositions method) test_gap4_split1() (seismicrna.core.mu.tests.unbias_test.TestFindSplitPositions method) test_gap_le_zero_le_npos() (seismicrna.core.mu.tests.unbias_test.TestAdjustMinGap method) test_generic_split() (seismicrna.core.mu.tests.unbias_test.TestFindSplitPositions method) test_get_alphaset() (seismicrna.core.seq.tests.xna_test.TestDNA method) (seismicrna.core.seq.tests.xna_test.TestRNA method) test_get_comp() (seismicrna.core.seq.tests.xna_test.TestDNA method) (seismicrna.core.seq.tests.xna_test.TestRNA method) test_get_comptrans() (seismicrna.core.seq.tests.xna_test.TestDNA method) (seismicrna.core.seq.tests.xna_test.TestRNA method) test_get_mask() (seismicrna.core.seq.tests.section_test.TestSectionMaskNames method) test_get_nonalphaset() (seismicrna.core.seq.tests.xna_test.TestDNA method) (seismicrna.core.seq.tests.xna_test.TestRNA method) test_hashable_dna() (seismicrna.core.seq.tests.xna_test.TestXNA method) test_hashable_rna() (seismicrna.core.seq.tests.xna_test.TestXNA method) test_hyphenate() (seismicrna.core.seq.tests.section_test.TestHyphenateEnds method) test_illegal_prefix() (seismicrna.core.seq.tests.fasta_test.TestValidFastaSeqname method) test_illegal_suffix() (seismicrna.core.seq.tests.fasta_test.TestValidFastaSeqname method) test_index() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_inequality_min_num_edits() (seismicrna.align.tests.xamgen_test.TestAlignmentScoreParams method) test_inequality_subst_vs_indel() (seismicrna.align.tests.xamgen_test.TestAlignmentScoreParams method) test_infer() (seismicrna.core.mu.tests.unbias_test.TestCalcParams method) test_insert_bare_invalid() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) test_insert_dangling_3_invalid() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) test_insert_dangling_5_invalid() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) test_insert_deletion_invalid() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) test_insert_end3_invalid() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) test_insert_end5_invalid() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) test_insert_non_match_valid() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) test_insert_valid() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) test_invalid_1() (seismicrna.core.tests.version_test.TestParseVersion method) test_invalid_2() (seismicrna.core.tests.version_test.TestParseVersion method) test_invalid_3() (seismicrna.core.tests.version_test.TestParseVersion method) test_invalid_4() (seismicrna.core.tests.version_test.TestParseVersion method) test_invalid_5() (seismicrna.core.tests.version_test.TestParseVersion method) test_invalid_bases() (seismicrna.core.seq.tests.xna_test.TestDNA method) (seismicrna.core.seq.tests.xna_test.TestRNA method) test_invalid_dim() (seismicrna.core.mu.tests.unbias_test.TestPublicCalcPNoCloseGivenEnds method) test_invalid_dup_1() (seismicrna.core.seq.tests.section_test.TestSeqPosToIndex method) test_invalid_empty_seq_1() (seismicrna.core.seq.tests.section_test.TestSeqPosToIndex method) test_invalid_empty_seq_2() (seismicrna.core.seq.tests.section_test.TestSeqPosToIndex method) test_invalid_empty_seq_3() (seismicrna.core.seq.tests.section_test.TestSeqPosToIndex method) test_invalid_full_0() (seismicrna.core.seq.tests.section_test.TestSeqPosToIndex method) test_invalid_greater_end_9() (seismicrna.core.seq.tests.section_test.TestSeqPosToIndex method) test_invalid_less_start_2() (seismicrna.core.seq.tests.section_test.TestSeqPosToIndex method) test_invalid_name() (seismicrna.core.seq.tests.fasta_test.TestParseFasta method) (seismicrna.core.seq.tests.fasta_test.TestWriteFasta method) test_invalid_noncontig() (seismicrna.core.seq.tests.section_test.TestIndexToSeq method) test_invalid_numeric() (seismicrna.core.tests.header_test.TestParseHeader method) test_invalid_pair() (seismicrna.core.rna.tests.db_test.TestFormatDbStructure method) (seismicrna.core.rna.tests.pair_test.TestDictToPairs method) test_invalid_pos3() (seismicrna.core.rna.tests.db_test.TestFormatDbStructure method) test_invalid_pos5() (seismicrna.core.rna.tests.db_test.TestFormatDbStructure method) test_invalid_position() (seismicrna.core.rna.tests.pair_test.TestDictToPairs method) (seismicrna.core.rna.tests.pair_test.TestPairsToDict method) test_invalid_position_1() (seismicrna.core.rna.tests.pair_test.TestPairsToTable method) test_invalid_position_2() (seismicrna.core.rna.tests.pair_test.TestPairsToTable method) test_invalid_quantiles() (seismicrna.core.mu.tests.scale_test.TestCalcQuantile method) test_invalid_seq() (seismicrna.core.seq.tests.fasta_test.TestParseFasta method) test_invalid_unsort_1() (seismicrna.core.seq.tests.section_test.TestSeqPosToIndex method) test_invert() (seismicrna.core.mu.tests.unbias_test.TestCalcPEnds method) (seismicrna.core.mu.tests.unbias_test.TestCalcPMutGivenSpan method) (seismicrna.core.tests.stats_test.TestCalcBetaParams method) (seismicrna.core.tests.stats_test.TestCalcDirichletParams method) test_is_inverse() (seismicrna.core.tests.array_test.TestCalcInverse method) test_iter_clust_indexes() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_kmers() (seismicrna.core.seq.tests.xna_test.TestDNA method) test_length_0() (seismicrna.core.batch.tests.count_test.TestCountEndCoords method) (seismicrna.core.mu.tests.unbias_test.TestPrivateCalcPNoCloseGivenEnds method) test_length_1() (seismicrna.core.batch.tests.count_test.TestCountEndCoords method) (seismicrna.core.mu.tests.unbias_test.TestPrivateCalcPNoCloseGivenEnds method) (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsAll method) test_length_2() (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsAll method) test_length_2_diff() (seismicrna.core.batch.tests.count_test.TestCountEndCoords method) test_length_2_min_gap_1() (seismicrna.core.mu.tests.unbias_test.TestPrivateCalcPNoCloseGivenEnds method) test_length_2_same() (seismicrna.core.batch.tests.count_test.TestCountEndCoords method) test_length_3() (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsAll method) test_length_3_diff_weights() (seismicrna.core.batch.tests.count_test.TestCountEndCoords method) test_length_3_min_gap_1() (seismicrna.core.mu.tests.unbias_test.TestPrivateCalcPNoCloseGivenEnds method) test_length_3_min_gap_2() (seismicrna.core.mu.tests.unbias_test.TestPrivateCalcPNoCloseGivenEnds method) test_length_3_same_weights() (seismicrna.core.batch.tests.count_test.TestCountEndCoords method) test_length_4_min_gap_1() (seismicrna.core.mu.tests.unbias_test.TestPrivateCalcPNoCloseGivenEnds method) test_length_4_min_gap_2() (seismicrna.core.mu.tests.unbias_test.TestPrivateCalcPNoCloseGivenEnds method) test_length_4_min_gap_3() (seismicrna.core.mu.tests.unbias_test.TestPrivateCalcPNoCloseGivenEnds method) test_level_keys() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_level_names() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_levels() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_line_in_sam_format() (seismicrna.align.tests.sim_test.TestAsSam method) test_locate_0() (seismicrna.core.tests.array_test.TestLocateElements method) test_locate_1() (seismicrna.core.tests.array_test.TestLocateElements method) test_locate_2() (seismicrna.core.tests.array_test.TestLocateElements method) test_locate_invalid() (seismicrna.core.tests.array_test.TestLocateElements method) test_low_qual() (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsQ53 method) test_low_qual_invalid() (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsQ53 method) test_low_qual_valid() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) test_mask() (seismicrna.core.batch.tests.ends_test.TestMaskSegmentEnds method) (seismicrna.core.batch.tests.ends_test.TestMergeSegmentEnds method) test_mask_gu() (seismicrna.core.seq.tests.section_test.TestSectionMaskGU method) test_mask_list() (seismicrna.core.seq.tests.section_test.TestSectionMaskList method) test_mask_names() (seismicrna.core.seq.tests.section_test.TestSectionMaskNames method) test_mask_polya() (seismicrna.core.seq.tests.section_test.TestSectionMaskPolyA method) test_masked_bool() (seismicrna.core.seq.tests.section_test.TestSectionMasked method) test_masked_int() (seismicrna.core.seq.tests.section_test.TestSectionMasked method) test_masked_zero() (seismicrna.core.seq.tests.section_test.TestSectionMasked method) test_match() (seismicrna.core.batch.tests.ends_test.TestMatchReadsSegments method) test_max_order() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestMakeHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_min_gap_0() (seismicrna.core.mu.tests.unbias_test.TestPrivateCalcPNoCloseGivenEnds method) test_min_order() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestMakeHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_misformatted() (seismicrna.core.seq.tests.fasta_test.TestValidFastaSeqname method) test_mismatch() (seismicrna.core.batch.tests.ends_test.TestMergeReadEnds method) test_missing_index_names() (seismicrna.core.tests.header_test.TestParseHeader method) test_missing_reverse_1() (seismicrna.core.rna.tests.pair_test.TestDictToPairs method) test_missing_reverse_2() (seismicrna.core.rna.tests.pair_test.TestDictToPairs method) test_missing_values() (seismicrna.core.tests.header_test.TestParseHeader method) test_modified_all() (seismicrna.core.tests.header_test.TestRelClustHeader method) test_modified_empty_rels() (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method)

test_modified_max_order() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_modified_max_order_0() (seismicrna.core.tests.header_test.TestRelClustHeader method) test_modified_min_order() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_modified_none() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_modified_nullified() (seismicrna.core.tests.header_test.TestRelClustHeader method) test_modified_rels() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_monopoly_1d() (seismicrna.core.mu.tests.measure_test.TestCalcGini method) test_more_clusters() (seismicrna.cluster.tests.compare_test.TestAssignClusterings method) test_more_muts() (seismicrna.core.mu.tests.unbias_test.TestNoCloseMuts method) test_multi_marks() (seismicrna.core.rna.tests.db_test.TestParseDbStructure method) test_multi_pseudoknot() (seismicrna.core.rna.tests.db_test.TestFormatDbStructure method) (seismicrna.core.rna.tests.db_test.TestParseDbStructure method) test_n() (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsQ53 method) test_n_segments_contig() (seismicrna.core.batch.tests.ends_test.TestSortSegmentEnds method) test_n_segments_discontig() (seismicrna.core.batch.tests.ends_test.TestSortSegmentEnds method) test_name_mark() (seismicrna.core.seq.tests.fasta_test.TestValidFastaSeqname method) test_names() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_nan() (seismicrna.core.mu.tests.scale_test.TestCalcRanks method) test_ncls1() (seismicrna.core.mu.tests.unbias_test.TestCalcPClustGivenNoClose method) test_ncls2() (seismicrna.core.mu.tests.unbias_test.TestCalcPClustGivenNoClose method) test_negative() (seismicrna.core.tests.array_test.TestCalcInverse method) (seismicrna.core.tests.header_test.TestListClusts method) test_negative_none() (seismicrna.core.tests.header_test.TestListOrders method) test_negative_positive() (seismicrna.core.tests.header_test.TestListOrders method) test_negative_zero() (seismicrna.core.tests.header_test.TestListOrders method) test_negative_zero_allowed() (seismicrna.core.tests.header_test.TestValidateOrderClust method) test_nested() (seismicrna.core.rna.tests.pair_test.TestFindEnclosingPairs method) test_no_gap3() (seismicrna.sim.tests.ends_test.TestSimEnds method) test_no_gap5() (seismicrna.sim.tests.ends_test.TestSimEnds method) test_no_muts() (seismicrna.core.mu.tests.unbias_test.TestNoCloseMuts method) test_no_overwrite() (seismicrna.core.seq.tests.fasta_test.TestWriteFasta method) test_no_pairs() (seismicrna.core.rna.tests.db_test.TestFormatDbStructure method) (seismicrna.core.rna.tests.db_test.TestParseDbStructure method) (seismicrna.core.rna.tests.pair_test.TestFindEnclosingPairs method) (seismicrna.core.rna.tests.pair_test.TestPairsToTable method) test_nocov_valid() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) test_nomask() (seismicrna.core.batch.tests.ends_test.TestMaskSegmentEnds method) (seismicrna.core.batch.tests.ends_test.TestMergeSegmentEnds method) test_non_array() (seismicrna.core.batch.tests.ends_test.TestCountReadsSegments method) test_none() (seismicrna.core.tests.header_test.TestMakeHeader method) (seismicrna.core.tests.header_test.TestParseHeader method) test_none_2d() (seismicrna.core.tests.array_test.TestFindDims method) test_nonnumeric() (seismicrna.core.tests.header_test.TestParseHeader method) test_normal() (seismicrna.core.rna.tests.pair_test.TestDictToPairs method) (seismicrna.core.rna.tests.pair_test.TestDictToTable method) (seismicrna.core.rna.tests.pair_test.TestPairsToDict method) (seismicrna.core.rna.tests.pair_test.TestPairsToTable method) (seismicrna.core.rna.tests.pair_test.TestTableToDict method) (seismicrna.core.rna.tests.pair_test.TestTableToPairs method) test_not_equal_dna_rna() (seismicrna.core.seq.tests.xna_test.TestXNA method) test_not_equal_dna_str() (seismicrna.core.seq.tests.xna_test.TestXNA method) test_not_equal_rna_str() (seismicrna.core.seq.tests.xna_test.TestXNA method) test_np_type() (seismicrna.core.rel.tests.code_test.TestConstants method) test_npos0_ncls1() (seismicrna.core.mu.tests.unbias_test.TestCalcPEndsGivenNoClose method) test_npos1_ncls0() (seismicrna.core.mu.tests.unbias_test.TestCalcPEndsGivenNoClose method) test_npos1_ncls1() (seismicrna.core.mu.tests.unbias_test.TestCalcPEndsGivenNoClose method) test_npos2_ncls1() (seismicrna.core.mu.tests.unbias_test.TestCalcPEndsGivenNoClose method) test_npos_le_zero_le_gap() (seismicrna.core.mu.tests.unbias_test.TestAdjustMinGap method) test_num_levels() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_one_degenerate() (seismicrna.core.seq.tests.xna_test.TestExpandDegenerateSeq method) test_one_full() (seismicrna.core.seq.tests.section_test.TestIntersect method) (seismicrna.core.seq.tests.section_test.TestUnite method) test_one_full_named() (seismicrna.core.seq.tests.section_test.TestIntersect method) (seismicrna.core.seq.tests.section_test.TestUnite method) test_one_invalid() (seismicrna.core.seq.tests.section_test.TestGetSharedIndex method) test_one_masked() (seismicrna.core.seq.tests.section_test.TestIntersect method) (seismicrna.core.seq.tests.section_test.TestUnite method) test_one_mut() (seismicrna.core.mu.tests.unbias_test.TestNoCloseMuts method) test_one_pair() (seismicrna.core.rna.tests.db_test.TestFormatDbStructure method) test_one_slice() (seismicrna.core.seq.tests.section_test.TestIntersect method) (seismicrna.core.seq.tests.section_test.TestUnite method) test_one_valid() (seismicrna.core.seq.tests.section_test.TestGetSharedIndex method) test_one_zero_allowed() (seismicrna.core.tests.header_test.TestValidateOrderClust method) test_one_zero_unallowed() (seismicrna.core.tests.header_test.TestValidateOrderClust method) test_order_name() (seismicrna.core.tests.header_test.TestConstants method) test_orders() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_other_dims() (seismicrna.core.tests.array_test.TestEnsureSameLength method) (seismicrna.core.tests.array_test.TestGetLength method) test_overhangs() (seismicrna.relate.py.tests.relate_test.TestMergeMates method) test_overwrite() (seismicrna.core.seq.tests.fasta_test.TestWriteFasta method) test_p_clust() (seismicrna.core.mu.tests.unbias_test.TestCalcPClust method) test_p_noclose() (seismicrna.core.mu.tests.unbias_test.TestCalcPNoClose method) test_paired_marks() (seismicrna.core.rna.tests.db_test.TestPairedMarks method) test_paired_reads_masked_segments() (seismicrna.core.batch.tests.muts_test.TestCalcMutsMatrix method) test_paired_reads_no_muts() (seismicrna.core.batch.tests.muts_test.TestCalcMutsMatrix method) test_parse_default() (seismicrna.core.tests.version_test.TestParseVersion method) test_parse_notag() (seismicrna.core.tests.version_test.TestParseVersion method) test_parse_prtag_letter() (seismicrna.core.tests.version_test.TestParseVersion method) test_parse_prtag_letters() (seismicrna.core.tests.version_test.TestParseVersion method) test_parse_prtag_letters_numbers() (seismicrna.core.tests.version_test.TestParseVersion method) test_partial_lengths() (seismicrna.core.seq.tests.section_test.TestSectionLength method) test_partial_reads_muts() (seismicrna.core.batch.tests.muts_test.TestCalcMutsMatrix method) test_partial_reads_no_muts() (seismicrna.core.batch.tests.muts_test.TestCalcMutsMatrix method) test_partial_reads_no_muts_some_masked() (seismicrna.core.batch.tests.muts_test.TestCalcMutsMatrix method) test_partial_reflen_equal() (seismicrna.core.seq.tests.section_test.TestSectionInit method) test_partial_reflen_greater() (seismicrna.core.seq.tests.section_test.TestSectionInit method) test_partial_reflen_less() (seismicrna.core.seq.tests.section_test.TestSectionInit method) test_partial_seq5_equal() (seismicrna.core.seq.tests.section_test.TestSectionInit method) test_partial_seq5_greater() (seismicrna.core.seq.tests.section_test.TestSectionInit method) test_partial_seq5_less() (seismicrna.core.seq.tests.section_test.TestSectionInit method) test_partial_seq5_reflen() (seismicrna.core.seq.tests.section_test.TestSectionInit method) test_partial_slice() (seismicrna.core.seq.tests.section_test.TestSectionInit method) test_partial_slice_invalid_end3() (seismicrna.core.seq.tests.section_test.TestSectionInit method) test_partial_slice_invalid_end5() (seismicrna.core.seq.tests.section_test.TestSectionInit method) test_partial_slice_invalid_reflen() (seismicrna.core.seq.tests.section_test.TestSectionInit method) test_partial_slice_invalid_seq5() (seismicrna.core.seq.tests.section_test.TestSectionInit method) test_partial_trunc_section_trunc_sub() (seismicrna.core.seq.tests.section_test.TestSubsection method) test_phreds() (seismicrna.core.ngs.tests.phred_test.TestConstants method) test_picto() (seismicrna.core.seq.tests.xna_test.TestDNA method) (seismicrna.core.seq.tests.xna_test.TestRNA method) test_pos_name() (seismicrna.core.seq.tests.section_test.TestConstants method) test_positive() (seismicrna.core.tests.header_test.TestFormatClustName method) (seismicrna.core.tests.header_test.TestListClusts method) (seismicrna.core.tests.header_test.TestListOrderClusts method) test_positive_invalid_dups() (seismicrna.core.tests.header_test.TestFormatClustNames method) test_positive_no_dups() (seismicrna.core.tests.header_test.TestFormatClustNames method) test_positive_none() (seismicrna.core.tests.header_test.TestListOrders method) (seismicrna.core.tests.header_test.TestListOrdersClusts method) test_positive_positive() (seismicrna.core.tests.header_test.TestListOrders method) (seismicrna.core.tests.header_test.TestListOrdersClusts method) (seismicrna.core.tests.header_test.TestValidateOrderClust method) test_positive_valid_dups() (seismicrna.core.tests.header_test.TestFormatClustNames method) test_positive_zero() (seismicrna.core.tests.header_test.TestListOrders method) test_primary_codes() (seismicrna.core.rel.tests.code_test.TestConstants method) test_pseudoknot() (seismicrna.core.rna.tests.db_test.TestFormatDbStructure method) (seismicrna.core.rna.tests.db_test.TestParseDbStructure method) test_pseudoknotted() (seismicrna.core.rna.tests.pair_test.TestFindEnclosingPairs method) test_quals() (seismicrna.core.ngs.tests.phred_test.TestConstants method) test_random() (seismicrna.core.seq.tests.xna_test.TestDNA method) (seismicrna.core.seq.tests.xna_test.TestRNA method) test_range() (seismicrna.core.seq.tests.section_test.TestSectionRange method) test_range_int() (seismicrna.core.seq.tests.section_test.TestSectionRange method) test_range_one() (seismicrna.core.seq.tests.section_test.TestSectionRange method) test_read1() (seismicrna.relate.py.tests.relate_test.TestMergeMates method) test_read2() (seismicrna.relate.py.tests.relate_test.TestMergeMates method) test_read_zero() (seismicrna.sim.tests.ends_test.TestSimEnds method) test_reduce_0() (seismicrna.core.mu.tests.frame_test.TestAutoReframe method) test_reduce_0_and_1() (seismicrna.core.mu.tests.frame_test.TestAutoReframe method) test_reduce_none() (seismicrna.core.mu.tests.frame_test.TestAutoReframe method) test_rel_index() (seismicrna.core.tests.header_test.TestParseHeader method) test_rel_index_invalid_name() (seismicrna.core.tests.header_test.TestParseHeader method) test_rel_index_repeated() (seismicrna.core.tests.header_test.TestParseHeader method) test_rel_index_valid_name() (seismicrna.core.tests.header_test.TestParseHeader method) test_rel_multiindex() (seismicrna.core.tests.header_test.TestParseHeader method) test_rel_name() (seismicrna.core.tests.header_test.TestConstants method) test_relclust() (seismicrna.core.tests.header_test.TestParseHeader method) test_relclustheaders() (seismicrna.core.tests.header_test.TestEqualHeaders method) test_relheaders() (seismicrna.core.tests.header_test.TestEqualHeaders method) test_rels() (seismicrna.core.tests.header_test.TestMakeHeader method) test_rels_duplicated() (seismicrna.core.tests.header_test.TestRelHeader method) test_rels_empty() (seismicrna.core.tests.header_test.TestRelHeader method) test_rels_normal() (seismicrna.core.tests.header_test.TestRelHeader method) test_repeat_pos3() (seismicrna.core.rna.tests.db_test.TestFormatDbStructure method) test_repeat_pos5() (seismicrna.core.rna.tests.db_test.TestFormatDbStructure method) test_repeated() (seismicrna.core.tests.array_test.TestCalcInverse method) test_reverse_complement() (seismicrna.core.seq.tests.xna_test.TestDNA method) (seismicrna.core.seq.tests.xna_test.TestRNA method) test_reverse_transcribe() (seismicrna.core.seq.tests.xna_test.TestRNA method) test_same_length() (seismicrna.core.tests.array_test.TestEnsureSameLength method) test_scipy_beta() (seismicrna.core.tests.stats_test.TestCalcBetaMV method) test_scipy_dirichlet() (seismicrna.core.tests.stats_test.TestCalcDirichletMV method) test_score_consistency() (seismicrna.align.tests.xamgen_test.TestAlignmentScoreParams method) test_select_clust() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) test_select_clusts() (seismicrna.core.tests.header_test.TestClustHeader method) test_select_extra() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_select_extra_emptystr() (seismicrna.core.tests.header_test.TestRelClustHeader method) test_select_extra_none() (seismicrna.core.tests.header_test.TestRelClustHeader method) test_select_extra_zero() (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_select_invalid() (seismicrna.core.tests.header_test.TestRelHeader method) test_select_invalid_clust() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) test_select_invalid_order() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) test_select_invalid_rel() (seismicrna.core.tests.header_test.TestRelClustHeader method) test_select_none() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_select_one_rels() (seismicrna.core.tests.header_test.TestRelHeader method) test_select_order() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) test_select_order_clust_empty() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) test_select_order_clust_exist() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) test_select_orders() (seismicrna.core.tests.header_test.TestClustHeader method) test_select_orders_clusts_exist() (seismicrna.core.tests.header_test.TestClustHeader method) test_select_rel() (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_select_two_rels() (seismicrna.core.tests.header_test.TestRelHeader method) test_seq_index_names() (seismicrna.core.seq.tests.section_test.TestConstants method) test_series() (seismicrna.core.mu.tests.compare_test.TestCalcNRMSD method) (seismicrna.core.mu.tests.compare_test.TestCalcPearson method) (seismicrna.core.mu.tests.compare_test.TestCalcSpearman method) (seismicrna.core.mu.tests.dim_test.TestCountPos method) (seismicrna.core.mu.tests.dim_test.TestCountsPos method) (seismicrna.core.mu.tests.frame_test.TestReframe method) (seismicrna.core.mu.tests.nan_test.TestAnyNaN method) (seismicrna.core.mu.tests.nan_test.TestNoNaN method) (seismicrna.core.mu.tests.nan_test.TestRemoveNaNs method) (seismicrna.core.mu.tests.nan_test.TestRemovesNaNs method) (seismicrna.core.mu.tests.scale_test.TestCalcQuantile method) (seismicrna.core.mu.tests.scale_test.TestCalcRanks method) (seismicrna.core.mu.tests.scale_test.TestCalcRMS method) (seismicrna.core.mu.tests.scale_test.TestNormalize method) (seismicrna.core.mu.tests.scale_test.TestStandardize method) (seismicrna.core.mu.tests.scale_test.TestWinsorize method) test_series_array() (seismicrna.core.mu.tests.frame_test.TestReframeLike method) test_series_series() (seismicrna.core.mu.tests.frame_test.TestReframeLike method) test_set_str_dna_rna() (seismicrna.core.seq.tests.xna_test.TestXNA method) test_shallow_pairs() (seismicrna.core.rna.tests.db_test.TestFormatDbStructure method) (seismicrna.core.rna.tests.db_test.TestParseDbStructure method) test_side3_equal_length() (seismicrna.align.tests.sim_test.TestFindBlankRange method) test_side3_neg_length() (seismicrna.align.tests.sim_test.TestFindBlankRange method) test_side3_over_length() (seismicrna.align.tests.sim_test.TestFindBlankRange method) test_side3_under_length() (seismicrna.align.tests.sim_test.TestFindBlankRange method) test_side3_zero_length() (seismicrna.align.tests.sim_test.TestFindBlankRange method) test_side5_equal_length() (seismicrna.align.tests.sim_test.TestFindBlankRange method) test_side5_neg_length() (seismicrna.align.tests.sim_test.TestFindBlankRange method) test_side5_over_length() (seismicrna.align.tests.sim_test.TestFindBlankRange method) test_side5_under_length() (seismicrna.align.tests.sim_test.TestFindBlankRange method) test_side5_zero_length() (seismicrna.align.tests.sim_test.TestFindBlankRange method) test_signature() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_simulated() (seismicrna.core.mu.tests.unbias_test.TestCalcPMutGivenSpanNoClose method) test_size() (seismicrna.core.seq.tests.section_test.TestSectionUnmasked method) (seismicrna.core.tests.header_test.TestRelHeader method) test_slice() (seismicrna.core.seq.tests.xna_test.TestDNA method) (seismicrna.core.seq.tests.xna_test.TestRNA method) test_slice_3x3() (seismicrna.core.mu.tests.unbias_test.TestSlicePEnds method) test_slice_5x5() (seismicrna.core.mu.tests.unbias_test.TestSlicePEnds method) test_slice_end3_equal() (seismicrna.core.seq.tests.section_test.TestSectionInit method) test_slice_end3_greater() (seismicrna.core.seq.tests.section_test.TestSectionInit method) test_slice_end3_less() (seismicrna.core.seq.tests.section_test.TestSectionInit method) test_slice_end5_end3() (seismicrna.core.seq.tests.section_test.TestSectionInit method) test_slice_end5_end3_invalid() (seismicrna.core.seq.tests.section_test.TestSectionInit method) test_slice_end5_equal() (seismicrna.core.seq.tests.section_test.TestSectionInit method) test_slice_end5_greater() (seismicrna.core.seq.tests.section_test.TestSectionInit method) test_slice_end5_less() (seismicrna.core.seq.tests.section_test.TestSectionInit method) test_slice_lengths() (seismicrna.core.seq.tests.section_test.TestSectionLength method) test_soft_clips() (seismicrna.relate.py.tests.relate_test.TestFindRelsLine method) test_subst_invalid() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) test_subst_valid() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) test_sum_positive() (seismicrna.core.mu.tests.unbias_test.TestNormalize method) test_sum_zero() (seismicrna.core.mu.tests.unbias_test.TestNormalize method) test_t() (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsQ53 method) test_three_overlapping() (seismicrna.core.seq.tests.section_test.TestIntersect method) test_thresh0() (seismicrna.core.mu.tests.unbias_test.TestFindSplitPositions method) test_thresh1() (seismicrna.core.mu.tests.unbias_test.TestFindSplitPositions method) test_threshold_0() (seismicrna.core.mu.tests.unbias_test.TestQuickUnbias method) test_threshold_0p001() (seismicrna.core.mu.tests.unbias_test.TestQuickUnbias method) test_to_array() (seismicrna.core.seq.tests.xna_test.TestDNA method) (seismicrna.core.seq.tests.xna_test.TestRNA method) test_transcribe() (seismicrna.core.seq.tests.xna_test.TestDNA method) test_tril() (seismicrna.core.mu.tests.unbias_test.TestTriuAllClose method) test_triu() (seismicrna.core.mu.tests.unbias_test.TestTriuAllClose method) test_trunc_section_full_sub() (seismicrna.core.seq.tests.section_test.TestSubsection method) test_trunc_section_trunc_sub() (seismicrna.core.seq.tests.section_test.TestSubsection method) test_two_degenerate() (seismicrna.core.seq.tests.xna_test.TestExpandDegenerateSeq method) test_two_disjoint() (seismicrna.core.seq.tests.section_test.TestIntersect method) (seismicrna.core.seq.tests.section_test.TestUnite method) test_two_disjoint_refseq() (seismicrna.core.seq.tests.section_test.TestUnite method) test_two_disjoint_wrong_refseq() (seismicrna.core.seq.tests.section_test.TestUnite method) test_two_full() (seismicrna.core.seq.tests.section_test.TestIntersect method) (seismicrna.core.seq.tests.section_test.TestUnite method) test_two_invalid() (seismicrna.core.seq.tests.section_test.TestGetSharedIndex method) test_two_masked() (seismicrna.core.seq.tests.section_test.TestIntersect method) (seismicrna.core.seq.tests.section_test.TestUnite method) test_two_overlapping() (seismicrna.core.seq.tests.section_test.TestIntersect method) (seismicrna.core.seq.tests.section_test.TestUnite method) test_two_overlapping_refseq() (seismicrna.core.seq.tests.section_test.TestUnite method) test_two_valid() (seismicrna.core.seq.tests.section_test.TestGetSharedIndex method) test_type() (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsQ53 method) test_typical() (seismicrna.sim.tests.ends_test.TestSimEnds method) test_unequal() (seismicrna.core.mu.tests.dim_test.TestCountsPosConsensus method) test_unmasked() (seismicrna.core.seq.tests.section_test.TestSectionUnmasked method) test_unmasked_bool() (seismicrna.core.seq.tests.section_test.TestSectionUnmasked method) test_unmasked_int() (seismicrna.core.seq.tests.section_test.TestSectionUnmasked method) test_unmasked_zero() (seismicrna.core.seq.tests.section_test.TestSectionUnmasked method) test_unpaired() (seismicrna.core.rna.tests.pair_test.TestConstants method) test_valid() (seismicrna.core.batch.tests.ends_test.TestCountReadsSegments method) (seismicrna.core.batch.tests.ends_test.TestMergeReadEnds method) (seismicrna.core.seq.tests.fasta_test.TestValidFastaSeqname method) (seismicrna.core.seq.tests.xna_test.TestDNA method) (seismicrna.core.seq.tests.xna_test.TestRNA method) (seismicrna.core.tests.header_test.TestIndexClusts method) (seismicrna.core.tests.header_test.TestIndexOrderClusts method) (seismicrna.core.tests.header_test.TestIndexOrders method) (seismicrna.core.tests.header_test.TestIndexOrdersClusts method) test_valid_blank_line() (seismicrna.core.seq.tests.fasta_test.TestParseFasta method) test_valid_dna() (seismicrna.core.seq.tests.fasta_test.TestParseFasta method) test_valid_empty() (seismicrna.core.seq.tests.fasta_test.TestParseFasta method) test_valid_empty_1() (seismicrna.core.seq.tests.section_test.TestSeqPosToIndex method) test_valid_empty_seq() (seismicrna.core.seq.tests.section_test.TestIndexToSeq method) (seismicrna.core.seq.tests.section_test.TestSeqPosToIndex method) test_valid_full() (seismicrna.core.seq.tests.section_test.TestIndexToPos method) (seismicrna.core.seq.tests.section_test.TestIndexToSeq method) test_valid_full_1() (seismicrna.core.seq.tests.section_test.TestSeqPosToIndex method) test_valid_full_9() (seismicrna.core.seq.tests.section_test.TestSeqPosToIndex method) test_valid_names() (seismicrna.core.seq.tests.fasta_test.TestParseFasta method) (seismicrna.core.seq.tests.fasta_test.TestWriteFasta method) test_valid_no_pos() (seismicrna.core.seq.tests.section_test.TestIndexToSeq method) test_valid_noncontig() (seismicrna.core.seq.tests.section_test.TestIndexToPos method) (seismicrna.core.seq.tests.section_test.TestIndexToSeq method) test_valid_noncontig_2() (seismicrna.core.seq.tests.section_test.TestSeqPosToIndex method) test_valid_rna() (seismicrna.core.seq.tests.fasta_test.TestParseFasta method) test_valid_slice() (seismicrna.core.seq.tests.section_test.TestIndexToPos method) (seismicrna.core.seq.tests.section_test.TestIndexToSeq method) test_valid_slice_6() (seismicrna.core.seq.tests.section_test.TestSeqPosToIndex method) test_var_zero() (seismicrna.sim.tests.ends_test.TestSimEnds method) test_vs_slow() (seismicrna.core.tests.array_test.TestFindTrueDists method) test_whole_numbers() (seismicrna.core.tests.array_test.TestTriangular method) test_window_0() (seismicrna.core.seq.tests.section_test.TestWindowToMargins method) test_window_float() (seismicrna.core.seq.tests.section_test.TestWindowToMargins method) test_window_length() (seismicrna.core.seq.tests.section_test.TestWindowToMargins method) test_window_margins() (seismicrna.core.seq.tests.section_test.TestWindowToMargins method) test_with_clip() (seismicrna.core.mu.tests.unbias_test.TestClip method) test_without_clip() (seismicrna.core.mu.tests.unbias_test.TestClip method) test_wrong_dims() (seismicrna.core.batch.tests.ends_test.TestCountReadsSegments method) (seismicrna.core.batch.tests.ends_test.TestMergeReadEnds method) test_xaax() (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsQ53 method) test_zero() (seismicrna.core.tests.header_test.TestListClusts method) (seismicrna.core.tests.header_test.TestListOrderClusts method) test_zero_degenerate() (seismicrna.core.seq.tests.xna_test.TestExpandDegenerateSeq method) test_zero_invalid() (seismicrna.core.seq.tests.section_test.TestGetSharedIndex method) test_zero_le_gap_lt_npos() (seismicrna.core.mu.tests.unbias_test.TestAdjustMinGap method) test_zero_lt_npos_le_gap() (seismicrna.core.mu.tests.unbias_test.TestAdjustMinGap method) test_zero_negative_allowed() (seismicrna.core.tests.header_test.TestValidateOrderClust method) test_zero_none() (seismicrna.core.tests.header_test.TestListOrders method) (seismicrna.core.tests.header_test.TestListOrdersClusts method) test_zero_one() (seismicrna.core.tests.header_test.TestListOrders method) (seismicrna.core.tests.header_test.TestListOrdersClusts method) test_zero_one_allowed() (seismicrna.core.tests.header_test.TestValidateOrderClust method) test_zero_one_unallowed() (seismicrna.core.tests.header_test.TestValidateOrderClust method) test_zero_two() (seismicrna.core.tests.header_test.TestListOrders method) test_zero_valid() (seismicrna.core.seq.tests.section_test.TestGetSharedIndex method) test_zero_zero() (seismicrna.core.tests.header_test.TestListOrders method) test_zero_zero_allowed() (seismicrna.core.tests.header_test.TestFormatClustName method) (seismicrna.core.tests.header_test.TestFormatClustNames method) (seismicrna.core.tests.header_test.TestValidateOrderClust method) test_zero_zero_unallowed() (seismicrna.core.tests.header_test.TestValidateOrderClust method) TestAdjustMinGap (class in seismicrna.core.mu.tests.unbias_test) TestAlignmentScoreParams (class in seismicrna.align.tests.xamgen_test) TestAnyNaN (class in seismicrna.core.mu.tests.nan_test) TestAsSam (class in seismicrna.align.tests.sim_test) TestAssignClusterings (class in seismicrna.cluster.tests.compare_test) TestAutoReframe (class in seismicrna.core.mu.tests.frame_test) TestAutoRemoveNaN (class in seismicrna.core.mu.tests.nan_test) TestAutoRemovesNaN (class in seismicrna.core.mu.tests.nan_test) TestCalcBetaMV (class in seismicrna.core.tests.stats_test) TestCalcBetaParams (class in seismicrna.core.tests.stats_test) TestCalcCoeffDeterm (class in seismicrna.core.mu.tests.compare_test) TestCalcCoverage (class in seismicrna.core.batch.tests.count_test) TestCalcDirichletMV (class in seismicrna.core.tests.stats_test) TestCalcDirichletParams (class in seismicrna.core.tests.stats_test) TestCalcGini (class in seismicrna.core.mu.tests.measure_test) TestCalcInverse (class in seismicrna.core.tests.array_test) TestCalcMutsMatrix (class in seismicrna.core.batch.tests.muts_test) TestCalcNRMSD (class in seismicrna.core.mu.tests.compare_test) TestCalcParams (class in seismicrna.core.mu.tests.unbias_test) TestCalcPClust (class in seismicrna.core.mu.tests.unbias_test) TestCalcPClustGivenNoClose (class in seismicrna.core.mu.tests.unbias_test) TestCalcPearson (class in seismicrna.core.mu.tests.compare_test) TestCalcPEnds (class in seismicrna.core.mu.tests.unbias_test) TestCalcPEndsGivenNoClose (class in seismicrna.core.mu.tests.unbias_test) TestCalcPEndsObserved (class in seismicrna.core.mu.tests.unbias_test) TestCalcPMutGivenSpan (class in seismicrna.core.mu.tests.unbias_test) TestCalcPMutGivenSpanNoClose (class in seismicrna.core.mu.tests.unbias_test) TestCalcPNoClose (class in seismicrna.core.mu.tests.unbias_test) TestCalcQuantile (class in seismicrna.core.mu.tests.scale_test) TestCalcRanks (class in seismicrna.core.mu.tests.scale_test) TestCalcRectangularSum (class in seismicrna.core.mu.tests.unbias_test) TestCalcRMS (class in seismicrna.core.mu.tests.scale_test) TestCalcSignalNoise (class in seismicrna.core.mu.tests.measure_test) TestCalcSpearman (class in seismicrna.core.mu.tests.compare_test) TestCalcUniqReadWeights (class in seismicrna.core.batch.tests.count_test) TestCheckNoCoverageReads (class in seismicrna.core.batch.tests.ends_test) TestCigarOp (class in seismicrna.relate.aux.tests.cigarop_test) TestClip (class in seismicrna.core.mu.tests.unbias_test) TestClustHeader (class in seismicrna.core.tests.header_test) TestCompareWindows (class in seismicrna.core.mu.tests.compare_test) TestConstants (class in seismicrna.core.ngs.tests.phred_test) (class in seismicrna.core.rel.tests.code_test) (class in seismicrna.core.rna.tests.pair_test) (class in seismicrna.core.seq.tests.section_test) (class in seismicrna.core.tests.header_test) TestCountCigarMuts (class in seismicrna.relate.aux.tests.cigarop_test) TestCountEndCoords (class in seismicrna.core.batch.tests.count_test) TestCountPos (class in seismicrna.core.mu.tests.dim_test) TestCountReadsSegments (class in seismicrna.core.batch.tests.ends_test) TestCountsPos (class in seismicrna.core.mu.tests.dim_test) TestCountsPosConsensus (class in seismicrna.core.mu.tests.dim_test) TestDecode (class in seismicrna.core.ngs.tests.phred_test) TestDictToPairs (class in seismicrna.core.rna.tests.pair_test) TestDictToTable (class in seismicrna.core.rna.tests.pair_test) TestDNA (class in seismicrna.core.seq.tests.xna_test) TestEncode (class in seismicrna.core.ngs.tests.phred_test) TestEncodeMatch (class in seismicrna.relate.py.tests.encode_test) TestEncodeRelate (class in seismicrna.relate.py.tests.encode_test) TestEnsureSameLength (class in seismicrna.core.tests.array_test) TestEqualHeaders (class in seismicrna.core.tests.header_test) TestExpandDegenerateSeq (class in seismicrna.core.seq.tests.xna_test) TestExpectation (class in seismicrna.cluster.tests.em_test) TestFindBlankRange (class in seismicrna.align.tests.sim_test) TestFindCigarOpPos (class in seismicrna.relate.aux.tests.cigarop_test) TestFindContiguousReads (class in seismicrna.core.batch.tests.ends_test) TestFindDims (class in seismicrna.core.tests.array_test) TestFindEnclosingPairs (class in seismicrna.core.rna.tests.pair_test) TestFindReadEnd3s (class in seismicrna.core.batch.tests.ends_test) TestFindReadEnd5s (class in seismicrna.core.batch.tests.ends_test) TestFindRelsLine (class in seismicrna.relate.py.tests.relate_test) TestFindSplitPositions (class in seismicrna.core.mu.tests.unbias_test) TestFindTrueDists (class in seismicrna.core.tests.array_test) TestFormat (class in seismicrna.core.seq.tests.fasta_test) TestFormatClustName (class in seismicrna.core.tests.header_test) TestFormatClustNames (class in seismicrna.core.tests.header_test) TestFormatDbStructure (class in seismicrna.core.rna.tests.db_test) TestFormatVersion (class in seismicrna.core.tests.version_test) TestGetComp (class in seismicrna.core.mu.tests.compare_test) TestGetLength (class in seismicrna.core.tests.array_test) TestGetSharedIndex (class in seismicrna.core.seq.tests.section_test) TestGetWindows (class in seismicrna.core.seq.tests.section_test) TestHeader (class in seismicrna.core.tests.header_test) TestHyphenateEnds (class in seismicrna.core.seq.tests.section_test) TestIndexClusts (class in seismicrna.core.tests.header_test) TestIndexOrderClusts (class in seismicrna.core.tests.header_test) TestIndexOrders (class in seismicrna.core.tests.header_test) TestIndexOrdersClusts (class in seismicrna.core.tests.header_test) TestIndexToPos (class in seismicrna.core.seq.tests.section_test) TestIndexToSeq (class in seismicrna.core.seq.tests.section_test) TestInferRead (class in seismicrna.relate.aux.tests.infer_test) TestIntersect (class in seismicrna.core.seq.tests.section_test) TestIterRelvecsAll (class in seismicrna.relate.aux.tests.iterrel_test) TestIterRelvecsQ53 (class in seismicrna.relate.aux.tests.iterrel_test) TestListClusts (class in seismicrna.core.tests.header_test) TestListOrderClusts (class in seismicrna.core.tests.header_test) TestListOrders (class in seismicrna.core.tests.header_test) TestListOrdersClusts (class in seismicrna.core.tests.header_test) TestLocateElements (class in seismicrna.core.tests.array_test) TestMakeHeader (class in seismicrna.core.tests.header_test) TestMaskSegmentEnds (class in seismicrna.core.batch.tests.ends_test) TestMatchReadsSegments (class in seismicrna.core.batch.tests.ends_test) TestMergeMates (class in seismicrna.relate.py.tests.relate_test) TestMergeReadEnds (class in seismicrna.core.batch.tests.ends_test) TestMergeSegmentEnds (class in seismicrna.core.batch.tests.ends_test) TestNoCloseMuts (class in seismicrna.core.mu.tests.unbias_test) TestNoNaN (class in seismicrna.core.mu.tests.nan_test) TestNormalize (class in seismicrna.core.mu.tests.scale_test) (class in seismicrna.core.mu.tests.unbias_test) TestPairedMarks (class in seismicrna.core.rna.tests.db_test) TestPairsToDict (class in seismicrna.core.rna.tests.pair_test) TestPairsToTable (class in seismicrna.core.rna.tests.pair_test) TestParseCigar (class in seismicrna.relate.py.tests.cigar_test) TestParseDbStructure (class in seismicrna.core.rna.tests.db_test) TestParseFasta (class in seismicrna.core.seq.tests.fasta_test) TestParseHeader (class in seismicrna.core.tests.header_test) TestParseVersion (class in seismicrna.core.tests.version_test) TestPrivateCalcPNoCloseGivenEnds (class in seismicrna.core.mu.tests.unbias_test) TestPublicCalcPNoCloseGivenEnds (class in seismicrna.core.mu.tests.unbias_test) TestQuickUnbias (class in seismicrna.core.mu.tests.unbias_test) TestReframe (class in seismicrna.core.mu.tests.frame_test) TestReframeLike (class in seismicrna.core.mu.tests.frame_test) TestRelClustHeader (class in seismicrna.core.tests.header_test) TestRelHeader (class in seismicrna.core.tests.header_test) TestRemoveNaNs (class in seismicrna.core.mu.tests.nan_test) TestRemovesNaNs (class in seismicrna.core.mu.tests.nan_test) TestRNA (class in seismicrna.core.seq.tests.xna_test) TestRunFASTQC (class in seismicrna.align.tests.fqutil_test) TestSectionAddMask (class in seismicrna.core.seq.tests.section_test) TestSectionCopy (class in seismicrna.core.seq.tests.section_test) TestSectionEqual (class in seismicrna.core.seq.tests.section_test) TestSectionInit (class in seismicrna.core.seq.tests.section_test) TestSectionLength (class in seismicrna.core.seq.tests.section_test) TestSectionMasked (class in seismicrna.core.seq.tests.section_test) TestSectionMaskGU (class in seismicrna.core.seq.tests.section_test) TestSectionMaskList (class in seismicrna.core.seq.tests.section_test) TestSectionMaskNames (class in seismicrna.core.seq.tests.section_test) TestSectionMaskPolyA (class in seismicrna.core.seq.tests.section_test) TestSectionRange (class in seismicrna.core.seq.tests.section_test) TestSectionUnmasked (class in seismicrna.core.seq.tests.section_test) TestSeqPosToIndex (class in seismicrna.core.seq.tests.section_test) TestSimEnds (class in seismicrna.sim.tests.ends_test) TestSlicePEnds (class in seismicrna.core.mu.tests.unbias_test) TestSortSegmentEnds (class in seismicrna.core.batch.tests.ends_test) TestStandardize (class in seismicrna.core.mu.tests.scale_test) TestSubsection (class in seismicrna.core.seq.tests.section_test) TestTableToDict (class in seismicrna.core.rna.tests.pair_test) TestTableToPairs (class in seismicrna.core.rna.tests.pair_test) TestTriangular (class in seismicrna.core.tests.array_test) TestTriuAllClose (class in seismicrna.core.mu.tests.unbias_test) TestTriuCumSum (class in seismicrna.core.mu.tests.unbias_test) TestTriuDiv (class in seismicrna.core.mu.tests.unbias_test) TestTriuDot (class in seismicrna.core.mu.tests.unbias_test) TestTriuLog (class in seismicrna.core.mu.tests.unbias_test) TestTriuNorm (class in seismicrna.core.mu.tests.unbias_test) TestTriuSum (class in seismicrna.core.mu.tests.unbias_test) TestUnite (class in seismicrna.core.seq.tests.section_test) TestValidateOrderClust (class in seismicrna.core.tests.header_test) TestValidFastaSeqname (class in seismicrna.core.seq.tests.fasta_test) TestWindowToMargins (class in seismicrna.core.seq.tests.section_test) TestWinsorize (class in seismicrna.core.mu.tests.scale_test) TestWriteFasta (class in seismicrna.core.seq.tests.fasta_test) TestXNA (class in seismicrna.core.seq.tests.xna_test) title (seismicrna.core.report.Field attribute) (seismicrna.core.report.OptionField attribute) (seismicrna.graph.base.GraphBase property) title_action_sample (seismicrna.graph.base.GraphBase property) (seismicrna.graph.onetable.OneTableGraph property) (seismicrna.graph.twotable.TwoTableGraph property) tmp_sam_path (seismicrna.relate.sam.XamViewer property) tmp_xam_cmd() (in module seismicrna.relate.sam) to_ct() (in module seismicrna.core.rna.io) to_db() (in module seismicrna.core.rna.io) to_dict() (seismicrna.core.report.Report method) (seismicrna.core.seq.section.Section method) to_dms() (seismicrna.core.rna.profile.RNAProfile method) to_fasta() (seismicrna.core.rna.profile.RNAProfile method) to_new() (seismicrna.align.fqunit.FastqUnit method) to_report_format() (seismicrna.core.rel.pattern.HalfRelPattern method) to_varna_color_file() (seismicrna.core.rna.profile.RNAProfile method) top (seismicrna.core.data.Dataset property) (seismicrna.core.data.LoadedDataset property) (seismicrna.core.data.MergedDataset property) (seismicrna.core.data.MultistepDataset property) (seismicrna.graph.base.GraphBase property) (seismicrna.graph.onetable.OneTableGraph property) (seismicrna.graph.twotable.TwoTableGraph property) (seismicrna.table.base.Table property) (seismicrna.table.calc.Tabulator property) (seismicrna.table.load.TableLoader property) (seismicrna.table.write.TableWriter property) tpr (seismicrna.graph.roc.ROCGraph property) tr() (seismicrna.core.seq.xna.DNA method) transpath() (in module seismicrna.core.path) transpaths() (in module seismicrna.core.path) triangular() (in module seismicrna.core.array) triu_log() (in module seismicrna.core.mu.unbias) tunneled (seismicrna.relate.py.ambindel.Indel property) TwoTableGraph (class in seismicrna.graph.twotable) TwoTableMergedGraph (class in seismicrna.graph.twotable) TwoTableRunner (class in seismicrna.graph.twotable) TwoTableWriter (class in seismicrna.graph.twotable) type (seismicrna.core.seq.xna.CompressedSeq property)

U

ULINE (seismicrna.core.logs.AnsiCode attribute) UnbiasDataset (class in seismicrna.core.data) UniqReads (class in seismicrna.cluster.uniq) unite() (in module seismicrna.core.seq.section) universal_input_params() (seismicrna.graph.base.GraphRunner class method) universal_output_params() (seismicrna.graph.base.GraphRunner class method) unmasked (seismicrna.cluster.em.EmClustering property) (seismicrna.core.seq.section.Section property) unmasked_bool (seismicrna.core.seq.section.Section property)

unmasked_int (seismicrna.core.seq.section.Section property) unmasked_zero (seismicrna.core.seq.section.Section property) update_batches() (in module seismicrna.cluster.addclust) (in module seismicrna.cluster.delclust) update_field() (in module seismicrna.cluster.addclust) (in module seismicrna.cluster.delclust) update_log_counts() (in module seismicrna.cluster.addclust) (in module seismicrna.cluster.delclust) update_report() (in module seismicrna.cluster.addclust) (in module seismicrna.cluster.delclust)

V

valid_fasta_seqname() (in module seismicrna.core.seq.fasta) validate() (seismicrna.core.path.Field method) validate_int() (in module seismicrna.core.path) validate_order_clust() (in module seismicrna.core.header) validate_str() (in module seismicrna.core.path) validate_top() (in module seismicrna.core.path) var_params() (seismicrna.graph.base.GraphRunner class method) (seismicrna.graph.corroll.RollingCorrelationRunner class method) (seismicrna.graph.hist.HistogramRunner class method) (seismicrna.graph.onestruct.StructOneTableRunner class method) (seismicrna.graph.roll.RollingRunner class method) (seismicrna.graph.twotable.TwoTableRunner class method)

verify_index_names() (in module seismicrna.core.seq.section) verify_proportions() (in module seismicrna.sim.muts) view_xam_cmd() (in module seismicrna.core.ngs.xam)

W

what() (seismicrna.graph.aucroll.RollingAUCGraph class method) (seismicrna.graph.base.GraphBase class method) (seismicrna.graph.corroll.RollingCorrelationGraph class method) (seismicrna.graph.delprof.DeltaProfileGraph class method) (seismicrna.graph.giniroll.RollingGiniGraph class method) (seismicrna.graph.histpos.PosHistogramGraph class method) (seismicrna.graph.histread.ReadHistogramGraph class method) (seismicrna.graph.profile.MultiRelsProfileGraph class method) (seismicrna.graph.profile.OneRelProfileGraph class method) (seismicrna.graph.roc.ROCGraph class method) (seismicrna.graph.scatter.ScatterPlotGraph class method) (seismicrna.graph.snrroll.RollingSNRGraph class method) WideDataset (class in seismicrna.core.data) window_to_margins() (in module seismicrna.core.seq.section) winsorize() (in module seismicrna.core.mu.scale) with_tmp_dir() (in module seismicrna.core.tmp) wrap() (seismicrna.core.logs.AnsiCode class method) write() (in module seismicrna.table.write) (seismicrna.graph.base.GraphBase method) (seismicrna.graph.base.GraphWriter method) (seismicrna.relate.write.RelationWriter method) (seismicrna.table.write.TableWriter method)

write_all() (in module seismicrna.relate.write) write_batches() (in module seismicrna.cluster.save) write_csv() (seismicrna.graph.base.GraphBase method) write_fasta() (in module seismicrna.core.seq.fasta) write_html() (seismicrna.graph.base.GraphBase method) write_log_counts() (in module seismicrna.cluster.csv) write_mode() (in module seismicrna.core.write) write_mus() (in module seismicrna.cluster.csv) write_one() (in module seismicrna.relate.write) write_pdf() (seismicrna.graph.base.GraphBase method) write_png() (seismicrna.graph.base.GraphBase method) write_props() (in module seismicrna.cluster.csv) write_single_run_table() (in module seismicrna.cluster.csv) write_svg() (seismicrna.graph.base.GraphBase method) write_tmp_ref_files() (in module seismicrna.align.write)

X

x_title (seismicrna.graph.base.GraphBase property) (seismicrna.graph.delprof.DeltaProfileGraph property) (seismicrna.graph.histrel.RelHistogramGraph property) (seismicrna.graph.profile.ProfileGraph property) (seismicrna.graph.roc.ROCGraph property) (seismicrna.graph.roll.RollingGraph property) (seismicrna.graph.scatter.ScatterPlotGraph property)

xam_paired() (in module seismicrna.core.ngs.xam) xam_to_fastq_cmd() (in module seismicrna.core.ngs.xam) xamgen_cmd() (in module seismicrna.align.xamops) XamViewer (class in seismicrna.relate.sam) XNA (class in seismicrna.core.seq.xna)

Y

y_title (seismicrna.graph.aucroll.RollingAUCGraph property) (seismicrna.graph.base.GraphBase property) (seismicrna.graph.corroll.RollingCorrelationGraph property) (seismicrna.graph.delprof.DeltaProfileGraph property) (seismicrna.graph.giniroll.RollingGiniGraph property) (seismicrna.graph.histpos.PosHistogramGraph property) (seismicrna.graph.histread.ReadHistogramGraph property) (seismicrna.graph.profile.ProfileGraph property) (seismicrna.graph.roc.ROCGraph property) (seismicrna.graph.scatter.ScatterPlotGraph property) (seismicrna.graph.snrroll.RollingSNRGraph property)

YELLOW (seismicrna.core.logs.AnsiCode attribute) yes (seismicrna.core.rel.pattern.RelPattern attribute)