bioinfo-pf-curie/geniac-demo-version-3.2.0.zip
bioinfo-pf-curie-geniac-demo-51de656
.github
ISSUE_TEMPLATE
bug_report.md
511 Bytes
new_feature.md
265 Bytes
PULL_REQUEST_TEMPLATE
merge_request_template.md
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.gitignore
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issue_templates
bug_report.md
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new_feature.md
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merge_request_templates
merge_request_template.md
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.gitmodules
108 Bytes
CHANGELOG
2.9 kB
LICENSE
21.8 kB
README.md
6.3 kB
assets
devMessage.txt
423 Bytes
geniacLogo.png
12.4 kB
metadata.tsv
32 Bytes
multiqcConfig.yaml
6.7 kB
workflowOnCompleteTemplate.html
2.3 kB
workflowOnCompleteTemplate.txt
877 Bytes
bin
README.md
70 Bytes
apCheckDesign.py
6.2 kB
apGlad.R
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apMqcHeader.py
4.5 kB
apMyscript.sh
113 Bytes
markdown_to_html.py
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scrape_software_versions.py
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someScript.sh
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conf
README.md
254 Bytes
base.config
527 Bytes
geniac.config
2.8 kB
genomes.config
431 Bytes
process.config
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test.config
1.1 kB
docs
README.md
283 Bytes
output.md
648 Bytes
profiles.md
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usage.md
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env
alpine.env
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geniac
main.nf
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modules
fromSource
CMakeLists.txt
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helloWorld
CMakeLists.txt
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main.cpp
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nextflow.config
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nf-modules
local
process
alpine.nf
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checkDesign.nf
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execBinScript.nf
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fastqc.nf
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getSoftwareVersions.nf
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glad.nf
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helloWorld.nf
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multiqc.nf
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outputDocumentation.nf
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renvInit.nf
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standardUnixCommand.nf
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trickySoftware.nf
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workflowSummaryMqc.nf
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subworkflow
myWorkflow0.nf
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myWorkflow1.nf
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recipes
conda
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renvGlad.yml
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trickySoftware.yml
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dependencies
README.md
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alpine
myDependency.sh
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renvGlad
renv.lock
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docker
README.md
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alpine.Dockerfile
188 Bytes
singularity
README.md
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alpine.def
276 Bytes
test
README.md
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data
README.md
41 Bytes
SRR1106775-25K_1.fastq.gz
2.2 MB
SRR1106775-25K_2.fastq.gz
2.2 MB
SRR1106776-25K_1.fastq.gz
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SRR1106776-25K_2.fastq.gz
2.1 MB
design.csv
63 Bytes
metadata.tsv
78 Bytes
misc
conf
geniac.config
2.9 kB
main.nf.misc
14.8 kB
modules
fromSource
CMakeLists.txt
2.6 kB
bamcmp
CMakeLists.txt
1.6 kB
bamcmp
INSTALL
1.2 kB
LICENSE
35.1 kB
Makefile
731 Bytes
README.md
1.5 kB
include
BamRecVector.h
449 Bytes
HTSFileWrapper.h
1.1 kB
SamReader.h
489 Bytes
util.h
430 Bytes
src
BamRecVector.cpp
1.5 kB
HTSFileWrapper.cpp
11.0 kB
SamReader.cpp
2.2 kB
bamcmp.cpp
19.5 kB
util.cpp
3.3 kB
bamcmp.sh
147 Bytes
htslib
INSTALL
12.3 kB
LICENSE
3.5 kB
Makefile
46.3 kB
NEWS
90.9 kB
README
2.7 kB
README.large_positions.md
7.8 kB
bcf_sr_sort.c
23.0 kB
bcf_sr_sort.h
3.9 kB
bgzf.c
82.0 kB
bgzip.1
6.3 kB
bgzip.c
19.4 kB
builddir_vars.mk.in
2.5 kB
config.h.in
4.4 kB
config.mk.in
3.8 kB
configure
210.8 kB
configure.ac
23.7 kB
cram
README
8.3 kB
cram.h
2.4 kB
cram_codecs.c
124.7 kB
cram_codecs.h
8.6 kB
cram_decode.c
125.4 kB
cram_decode.h
3.7 kB
cram_encode.c
143.3 kB
cram_encode.h
3.7 kB
cram_external.c
27.0 kB
cram_index.c
23.6 kB
cram_index.h
3.9 kB
cram_io.c
174.4 kB
cram_io.h
18.2 kB
cram_samtools.h
2.9 kB
cram_stats.c
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cram_stats.h
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cram_structs.h
29.6 kB
mFILE.c
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mFILE.h
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misc.h
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open_trace_file.c
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open_trace_file.h
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os.h
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pooled_alloc.c
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pooled_alloc.h
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string_alloc.c
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string_alloc.h
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errmod.c
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faidx.5
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faidx.c
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header.c
80.2 kB
header.h
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hfile.c
40.0 kB
hfile_gcs.c
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hfile_internal.h
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hfile_libcurl.c
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hfile_s3.c
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hfile_s3_write.c
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hts.c
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hts_expr.c
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hts_internal.h
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hts_os.c
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hts_probe_cc.sh
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hts_time_funcs.h
5.9 kB
htscodecs
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8.4 kB
LICENSE.md
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MAINTAINERS.md
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NEWS.md
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htscodecs
arith_dynamic.c
35.7 kB
arith_dynamic.h
2.5 kB
c_range_coder.h
3.5 kB
c_simple_model.h
5.6 kB
fqzcomp_qual.c
49.0 kB
fqzcomp_qual.h
6.2 kB
htscodecs.c
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htscodecs.h
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htscodecs_endian.h
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pack.c
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pack.h
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permute.h
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pooled_alloc.h
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rANS_byte.h
18.6 kB
rANS_static.c
25.0 kB
rANS_static.h
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rANS_static16_int.h
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rANS_static32x16pr.c
24.9 kB
rANS_static32x16pr.h
8.3 kB
rANS_static32x16pr_avx2.c
64.8 kB
rANS_static32x16pr_avx512.c
39.2 kB
rANS_static32x16pr_neon.c
75.3 kB
rANS_static32x16pr_sse4.c
70.6 kB
rANS_static4x16.h
4.2 kB
rANS_static4x16pr.c
52.9 kB
rANS_word.h
16.5 kB
rle.c
6.8 kB
rle.h
3.8 kB
tokenise_name3.c
61.3 kB
tokenise_name3.h
2.6 kB
utils.c
7.6 kB
utils.h
11.8 kB
varint.h
12.4 kB
varint2.h
9.7 kB
version.h
39 Bytes
tests
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arith_dynamic_fuzz.c
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arith_dynamic_test.c
8.9 kB
benchmark.sh
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dat
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u32.9
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fqzcomp
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q4.1
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qvar.0
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qvar.1
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u32
52.2 kB
entropy.c
8.6 kB
entropy.test
221 Bytes
fqzcomp.test
764 Bytes
fqzcomp_qual_fuzz.c
3.0 kB
fqzcomp_qual_test.c
14.2 kB
names
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45.9 kB
02.names
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tok3
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nv.names.9
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nv2.names.1
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nv2.names.11
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nv2.names.13
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nv2.names.15
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nv2.names.17
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nv2.names.19
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nv2.names.3
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nv2.names.5
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nv2.names.7
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nv2.names.9
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rr.names.1
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rANS_static4x16pr_test.c
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rANS_static_fuzz.c
3.9 kB
rANS_static_test.c
8.7 kB
rans4x16.test
2.6 kB
rans4x8.test
763 Bytes
tok3.test
723 Bytes
tokenise_name3_fuzz.c
2.9 kB
tokenise_name3_test.c
6.4 kB
varint_test.c
10.3 kB
htscodecs_bundled.mk
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htscodecs_external.mk
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htsfile.1
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htsfile.c
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htslib
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16.5 kB
cram.h
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faidx.h
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hfile.h
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hts.h
57.4 kB
hts_defs.h
4.0 kB
hts_endian.h
11.7 kB
hts_expr.h
6.0 kB
hts_log.h
4.0 kB
hts_os.h
2.8 kB
kbitset.h
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kfunc.h
2.8 kB
khash.h
22.9 kB
khash_str2int.h
4.0 kB
klist.h
5.1 kB
knetfile.h
3.7 kB
kroundup.h
3.3 kB
kseq.h
9.2 kB
ksort.h
11.5 kB
kstring.h
11.5 kB
regidx.h
8.9 kB
sam.h
91.6 kB
synced_bcf_reader.h
16.6 kB
tbx.h
5.0 kB
thread_pool.h
12.7 kB
vcf.h
68.4 kB
vcf_sweep.h
1.7 kB
vcfutils.h
4.9 kB
htslib-s3-plugin.7
7.3 kB
htslib.map
12.8 kB
htslib.mk
6.8 kB
htslib.pc.in
490 Bytes
htslib_vars.mk
3.3 kB
kfunc.c
10.9 kB
kstring.c
10.6 kB
m4
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hts_hide_dynamic_syms.m4
2.6 kB
hts_prog_cc_warnings.m4
8.3 kB
pkg.m4
10.2 kB
md5.c
10.7 kB
multipart.c
8.5 kB
os
lzma_stub.h
2.3 kB
rand.c
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plugin.c
6.5 kB
probaln.c
17.3 kB
realn.c
13.2 kB
regidx.c
19.9 kB
region.c
7.7 kB
sam.5
2.8 kB
sam.c
194.8 kB
sam_internal.h
3.5 kB
sam_mods.c
25.2 kB
samples
DEMO.md
61.1 kB
Makefile
2.7 kB
add_header.c
4.0 kB
cram.c
6.7 kB
dump_aux.c
6.8 kB
flags_demo.c
3.5 kB
flags_htsopt_field.c
3.7 kB
index_multireg_read.c
4.5 kB
index_reg_read.c
4.4 kB
index_write.c
5.3 kB
mod_aux.c
7.3 kB
mod_aux_ba.c
4.2 kB
mod_bam.c
8.1 kB
modstate.c
6.4 kB
mpileup.c
6.7 kB
pileup.c
6.1 kB
pileup_mod.c
7.3 kB
read_aux.c
7.3 kB
read_bam.c
5.4 kB
read_fast.c
3.6 kB
read_header.c
5.1 kB
read_refname.c
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rem_header.c
4.2 kB
sample.ref.fa
106 Bytes
sample.sam
1.3 kB
split.c
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split2.c
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split_thread1.c
5.2 kB
split_thread2.c
5.4 kB
update_header.c
4.0 kB
write_fast.c
3.2 kB
synced_bcf_reader.c
48.7 kB
tabix.1
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tabix.c
26.3 kB
tbx.c
16.2 kB
test
auxf#values.sam
751 Bytes
auxf#values_java.cram
5.2 kB
auxf.fa
29 Bytes
auxf.fa.fai
18 Bytes
base_mods
MM-MNf1.sam
739 Bytes
MM-MNf2.sam
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MM-MNp.sam
739 Bytes
MM-chebi.out
372 Bytes
MM-chebi.sam
176 Bytes
MM-double.out
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MM-double.sam
254 Bytes
MM-explicit-f.out
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MM-explicit-x.out
791 Bytes
MM-explicit.out
768 Bytes
MM-explicit.sam
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MM-multi.out
765 Bytes
MM-multi.sam
537 Bytes
MM-not-all-modded.out
1.1 kB
MM-not-all-modded.sam
558 Bytes
MM-orient.sam
510 Bytes
MM-pileup.out
713 Bytes
MM-pileup.sam
723 Bytes
MM-pileup2.out
518 Bytes
MM-pileup2.sam
372 Bytes
base-mods.sh
1.3 kB
base-mods.tst
2.6 kB
bcf-sr
merge.noidx.a.vcf
518 Bytes
merge.noidx.abc.expected.out
128 Bytes
merge.noidx.b.vcf
634 Bytes
merge.noidx.c.vcf
634 Bytes
merge.noidx.hdr_order.vcf
518 Bytes
merge.noidx.rec_order.vcf
518 Bytes
weird-chr-names.1.out
217 Bytes
weird-chr-names.2.out
201 Bytes
weird-chr-names.3.out
221 Bytes
weird-chr-names.4.out
203 Bytes
weird-chr-names.5.out
225 Bytes
weird-chr-names.6.out
205 Bytes
weird-chr-names.vcf
241 Bytes
bgziptest.txt
15 Bytes
bgziptest.txt.gz
181 Bytes
bgziptest.txt.gz.gzi
88 Bytes
c1#bounds.sam
148 Bytes
c1#clip.sam
337 Bytes
c1#noseq.sam
433 Bytes
c1#pad1.sam
388 Bytes
c1#pad2.sam
527 Bytes
c1#pad3.sam
665 Bytes
c1#unknown.sam
429 Bytes
c1.fa
15 Bytes
c1.fa.fai
14 Bytes
c2#pad.sam
847 Bytes
c2.fa
14 Bytes
c2.fa.fai
12 Bytes
ce#1.sam
341 Bytes
ce#1000.sam
322.6 kB
ce#2.sam
645 Bytes
ce#5.sam
1.9 kB
ce#5b.sam
1.8 kB
ce#5b_java.cram
6.8 kB
ce#large_seq.sam
2.1 MB
ce#supp.sam
547 Bytes
ce#tag_depadded.sam
1.6 kB
ce#tag_padded.sam
1.6 kB
ce#unmap.sam
1.3 kB
ce#unmap1.sam
2.7 kB
ce#unmap2.sam
5.5 kB
ce.fa
1.1 MB
ce.fa.fai
230 Bytes
colons.bam
268 Bytes
colons.bam.bai
424 Bytes
compare_sam.pl
6.5 kB
cross_validate.sh
4.3 kB
emptyfile
0 Bytes
faidx
ce.1.expected.fa
326 Bytes
faidx.1.expected.fa
94 Bytes
faidx.fa
289 Bytes
faidx.fa.expected.fai
117 Bytes
faidx.tst
4.4 kB
fastqs.1.expected.fq
336 Bytes
fastqs.2.expected.fa
225 Bytes
fastqs.fq
48.6 kB
fastqs.fq.expected.fai
3.8 kB
test-faidx.sh
1.3 kB
fastq
fastq.tst
4.5 kB
filter_casava-q.sam
667 Bytes
filter_casava.fa
596 Bytes
filter_casava.fq
1.0 kB
filter_casava.sam
1.1 kB
inter_aux-q.sam
1.8 kB
inter_aux.sam
2.8 kB
inter_casava-q.sam
1.7 kB
inter_casava.sam
2.7 kB
inter_casavaOX-q.sam
1.7 kB
inter_casavaOX.sam
2.7 kB
inter_noaux-q.sam
1.5 kB
inter_noaux.sam
2.5 kB
interleaved.fa
1.6 kB
interleaved.fq
2.6 kB
interleaved_casava.fa
1.5 kB
interleaved_casava.fq
2.5 kB
longline.fq
1.1 kB
longline.sam
1.1 kB
minimal-q.sam
22 Bytes
minimal.fa
5 Bytes
minimal.fq
9 Bytes
minimal.sam
22 Bytes
multiline-q.sam
126 Bytes
multiline.fa
98 Bytes
multiline.fq
188 Bytes
multiline.sam
202 Bytes
name2-q.sam
512 Bytes
name2.fa
482 Bytes
name2.fq
894 Bytes
name2.sam
908 Bytes
r1-q.sam
950 Bytes
r1.fa
870 Bytes
r1.fq
1.4 kB
r1.sam
1.4 kB
r2-q.sam
815 Bytes
r2.fa
730 Bytes
r2.fq
1.2 kB
r2.sam
1.3 kB
single.fa
720 Bytes
single.fq
1.2 kB
single_aux-q.sam
805 Bytes
single_aux.sam
1.3 kB
single_noaux-q.sam
755 Bytes
single_noaux.sam
1.2 kB
test-fastq.sh
1.3 kB
fastqs_README.txt
5.0 kB
fieldarith.c
2.4 kB
fieldarith.sam
910 Bytes
formatcols.vcf
241 Bytes
formatmissing-out.vcf
226 Bytes
formatmissing.vcf
226 Bytes
fuzz
hts_open_fuzzer.c
4.0 kB
header_syms.pl
3.6 kB
hfile.c
12.0 kB
hts_endian.c
17.6 kB
index.bam.bai
776 Bytes
index.bam.csi
130 Bytes
index.bcf.csi
144 Bytes
index.cram.crai
83 Bytes
index.sam
54.2 kB
index.sam.gz.bai
776 Bytes
index.sam.gz.csi
130 Bytes
index.vcf
68.9 kB
index.vcf.gz.csi
168 Bytes
index.vcf.gz.tbi
206 Bytes
index2.sam
477 Bytes
index_dos.sam
54.4 kB
longrefs
index.expected1.vcf
594 Bytes
index.expected2.vcf
83 Bytes
index.vcf
21.5 kB
longref.sam
31.7 kB
longref_itr.expected.sam
8.3 kB
longref_multi.expected.sam
15.0 kB
maintainer
check_copyright.pl
3.3 kB
check_spaces.pl
2.7 kB
md#1.sam
1.0 kB
md.fa
45 Bytes
md.fa.fai
13 Bytes
modhdr.expected.vcf
148 Bytes
modhdr.vcf.gz
156 Bytes
modhdr.vcf.gz.csi
86 Bytes
mpileup
c1#pad1.out
274 Bytes
c1#pad1.sam
2.0 kB
c1#pad2.out
355 Bytes
c1#pad2.sam
2.3 kB
c1#pad3.out
134 Bytes
c1#pad3.sam
2.4 kB
mp_D.out
130 Bytes
mp_D.sam
1.5 kB
mp_DI.out
197 Bytes
mp_DI.sam
1.7 kB
mp_I.out
135 Bytes
mp_I.sam
1.8 kB
mp_ID.out
181 Bytes
mp_ID.sam
2.0 kB
mp_N.out
122 Bytes
mp_N.sam
1.7 kB
mp_N2.out
275 Bytes
mp_N2.sam
2.2 kB
mp_P.out
169 Bytes
mp_P.sam
1.8 kB
mpileup.tst
2.6 kB
small.bam
1.3 kB
small.out
3.3 kB
test-pileup.sh
1.3 kB
no_hdr_sq_1.bam
1.7 kB
no_hdr_sq_1.bam.csi
94 Bytes
no_hdr_sq_1.expected.sam
2.0 kB
noroundtrip-out.vcf
325 Bytes
noroundtrip.vcf
271 Bytes
pileup.c
7.0 kB
pileup_mod.c
7.1 kB
plugins-dlhts.c
5.1 kB
range.bam
13.3 kB
range.bam.bai
360 Bytes
range.cram
11.2 kB
range.cram.crai
94 Bytes
range.out
3.5 kB
realn01.fa
719 Bytes
realn01.fa.fai
21 Bytes
realn01.sam
1.8 kB
realn01_exp-a.sam
2.2 kB
realn01_exp-e.sam
2.2 kB
realn01_exp.sam
2.2 kB
realn02-r.sam
3.8 kB
realn02.fa
4.3 kB
realn02.fa.fai
17 Bytes
realn02.sam
2.9 kB
realn02_exp-a.sam
3.8 kB
realn02_exp-e.sam
3.8 kB
realn02_exp.sam
3.8 kB
realn03.fa
16 Bytes
realn03.fa.fai
14 Bytes
realn03.sam
138 Bytes
realn03_exp.sam
172 Bytes
sam.c
82.4 kB
sam_filter
filter.sh
1.3 kB
filter.tst
2.9 kB
func1.out
2 Bytes
func2.out
3 Bytes
func3.out
2 Bytes
func4.out
4 Bytes
func5.out
1.6 kB
func6.out
585 Bytes
func7.out
946 Bytes
int1.out
3 Bytes
int2.out
3 Bytes
int3.out
3 Bytes
string1.out
485 Bytes
string2.out
451 Bytes
string3.out
748 Bytes
string4.out
1.1 kB
string5.out
498 Bytes
string6.out
319 Bytes
string7.out
410 Bytes
simple_test_driver.sh
5.7 kB
tabix
bed_file.Y.100200.out
47 Bytes
bed_file.bed
1.9 kB
bed_file.separate.out
407 Bytes
gff_file.X.2934832.2935190.out
405 Bytes
gff_file.gff
5.6 kB
large_chr.20.1.2147483647.out
288 Bytes
large_chr.vcf
622 Bytes
tabix.tst
3.0 kB
test-tabix.sh
1.3 kB
vcf_file.1.3000151.out
67 Bytes
vcf_file.2.3199812.out
74 Bytes
vcf_file.bcf
4.5 kB
vcf_file.vcf
4.3 kB
tabix.out
98 Bytes
test-bcf-sr.c
9.5 kB
test-bcf-sr.pl
17.4 kB
test-bcf-translate.c
9.0 kB
test-bcf-translate.out
869 Bytes
test-bcf_set_variant_type.c
4.0 kB
test-logging.pl
2.6 kB
test-parse-reg.c
7.1 kB
test-regidx.c
17.0 kB
test-vcf-api.c
25.6 kB
test-vcf-api.out
2.1 kB
test-vcf-hdr-in.vcf
2.0 kB
test-vcf-hdr.out
1.3 kB
test-vcf-sweep.c
3.8 kB
test-vcf-sweep.out
92 Bytes
test.pl
47.6 kB
test_bgzf.c
35.6 kB
test_expr.c
12.5 kB
test_faidx.c
16.6 kB
test_index.c
2.9 kB
test_introspection.c
3.3 kB
test_kfunc.c
3.6 kB
test_kstring.c
12.1 kB
test_mod.c
7.6 kB
test_realn.c
5.1 kB
test_str2int.c
8.9 kB
test_time_funcs.c
4.6 kB
test_view.c
14.9 kB
thrash_threads1.c
1.7 kB
thrash_threads2.c
1.6 kB
thrash_threads3.c
1.7 kB
thrash_threads4.c
2.3 kB
thrash_threads5.c
2.2 kB
thrash_threads6.c
3.4 kB
thrash_threads7.c
3.7 kB
thread_pool.md
2.9 kB
vcf_meta_meta.vcf
427 Bytes
with-shlib.sh
2.1 kB
xx#MD.sam
1.1 kB
xx#MD2.sam
1.2 kB
xx#blank.sam
71 Bytes
xx#large_aux.sam
905.5 kB
xx#large_aux2.sam
651 Bytes
xx#large_aux_java.cram
22.7 kB
xx#minimal.sam
254 Bytes
xx#pair.sam
304 Bytes
xx#repeated.sam
298 Bytes
xx#rg.sam
517 Bytes
xx#tlen.sam
1.0 kB
xx#tlen2.sam
1.1 kB
xx#triplet.sam
267 Bytes
xx#unsorted.sam
320 Bytes
xx.fa
86 Bytes
xx.fa.fai
44 Bytes
textutils.c
12.0 kB
textutils_internal.h
14.9 kB
thread_pool.c
45.7 kB
thread_pool_internal.h
5.9 kB
vcf.5
3.5 kB
vcf.c
182.4 kB
vcf_sweep.c
5.6 kB
vcfutils.c
34.9 kB
version.sh
2.2 kB
fastqpair
.gitignore
483 Bytes
.travis.yml
99 Bytes
CITATION.md
2.1 kB
CMakeLists.txt
218 Bytes
INSTALLATION.md
1.3 kB
LICENSE
1.1 kB
README.md
5.2 kB
VERSION
4 Bytes
fastq_pair.c
9.3 kB
fastq_pair.h
1.1 kB
main.c
2.3 kB
robstr.c
1.0 kB
robstr.h
640 Bytes
test
left.fastq
257.7 kB
left_R1.fastq
261.6 kB
right.fastq
79.6 kB
right_R2.fastq
80.7 kB
nf-modules
local
process
bamcmp.nf.misc
1.1 kB
fastqpair.nf.misc
1.1 kB
samplePlan.csv
196 Bytes