bcgsc/mavis-v2.2.12.zip
bcgsc-mavis-861eed4
.coveragerc
111 Bytes
.github
CONTRIBUTING.md
3.5 kB
ISSUE_TEMPLATE
bug_report.md
771 Bytes
feature_request.md
604 Bytes
workflows
build.yml
2.8 kB
publish.yml
886 Bytes
.gitignore
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.pylintrc
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.readthedocs.yml
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LICENSE
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MANIFEST.in
247 Bytes
README.md
5.6 kB
bootstrap.py
7.5 kB
buildout.cfg
90 Bytes
codecov.yml
90 Bytes
docs
background
citations.md
2.5 kB
theory.md
16.4 kB
configuration
general.md
3.2 kB
performance.md
1.5 kB
pipeline.md
4.8 kB
settings.md
26.6 kB
development.md
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extra.css
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glossary.md
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hooks.py
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images
ENSG00000139687_RB1_overlay.png
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Fusion-ext.gpl
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GIMAP4_IL7_fusion.svg
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UBE2V2_GIMAP4_disruptive_fusion.svg
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acronym.svg
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annotation_case_dup.svg
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annotation_case_indel.svg
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annotation_case_inversion.svg
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annotation_model.svg
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annotations_summary.svg
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breakpoint_comparison_model.svg
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breakpoint_prediction_exonic.svg
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call_breakpoint_by_flanking_reads.svg
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classification_tree.svg
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colo829_tumour_annotation_resource_req.png
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colo829_tumour_validation_resource_req.png
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compatible_flanking_pairs.svg
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example_figure.svg
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feature_levels.svg
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flanking_pairs_fragment_sizes_deletion.svg
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fragment_sizes_histogram.svg
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get_app-24px.svg
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icon.png
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pipeline_dependency_graph.svg
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pipeline_options.svg
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read_evidence.svg
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read_pair_definitions.svg
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read_pairs_deletion.svg
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read_pairs_duplication.svg
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read_pairs_insertion.svg
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read_pairs_inversion_LL.svg
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read_pairs_inversion_RR.svg
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read_pairs_translocated_inversion_LL.svg
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read_pairs_translocated_inversion_RR.svg
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read_pairs_translocation_LR.svg
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read_pairs_translocation_RL.svg
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read_pairs_vs_contigs_evidence.svg
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splicing_model.svg
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splicing_pattern_default.svg
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splicing_pattern_multiple_acceptors.svg
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splicing_pattern_multiple_donors.svg
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index.md
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inputs
reference.md
9.8 kB
standard.md
5.1 kB
support.md
10.1 kB
outputs
columns.md
12.4 kB
illustrations.md
1.2 kB
index.md
124 Bytes
package
mavis
annotate
index.md
2.2 kB
cluster
index.md
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pairing
index.md
1.1 kB
summary
index.md
392 Bytes
validate
index.md
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tutorials
full.md
10.5 kB
mini.md
5.5 kB
env
example.sh
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generate_ensembl79_annotations.sh
996 Bytes
mavis
__init__.py
134 Bytes
align.py
25.3 kB
annotate
__init__.py
0 Bytes
base.py
7.4 kB
constants.py
2.8 kB
file_io.py
21.4 kB
fusion.py
27.4 kB
genomic.py
24.6 kB
main.py
12.7 kB
protein.py
16.1 kB
splicing.py
8.4 kB
variant.py
35.7 kB
assemble.py
18.6 kB
bam
__init__.py
0 Bytes
cache.py
11.0 kB
cigar.py
18.3 kB
read.py
20.9 kB
stats.py
10.3 kB
blat.py
16.7 kB
breakpoint.py
20.3 kB
cluster
__init__.py
44 Bytes
cluster.py
14.8 kB
constants.py
1.8 kB
main.py
9.9 kB
config.py
29.6 kB
constants.py
25.8 kB
error.py
341 Bytes
illustrate
__init__.py
0 Bytes
constants.py
8.7 kB
diagram.py
18.0 kB
elements.py
38.7 kB
scatter.py
8.1 kB
util.py
9.3 kB
interval.py
19.2 kB
main.py
22.0 kB
pairing
__init__.py
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constants.py
1.6 kB
main.py
5.7 kB
pairing.py
11.3 kB
schedule
__init__.py
0 Bytes
constants.py
3.9 kB
job.py
9.7 kB
local.py
5.6 kB
pipeline.py
39.4 kB
scheduler.py
34.1 kB
summary
__init__.py
0 Bytes
constants.py
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main.py
16.1 kB
summary.py
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tools
__init__.py
10.7 kB
arriba.py
1.5 kB
breakdancer.py
925 Bytes
chimerascan.py
1.5 kB
cnvnator.py
1.2 kB
constants.py
1.5 kB
starfusion.py
999 Bytes
transabyss.py
3.1 kB
vcf.py
11.1 kB
util.py
18.8 kB
validate
__init__.py
0 Bytes
base.py
49.3 kB
call.py
47.1 kB
constants.py
9.5 kB
evidence.py
16.8 kB
main.py
16.1 kB
mkdocs.yml
375 Bytes
requirements.txt
2 Bytes
setup.cfg
341 Bytes
setup.py
3.5 kB
tab
__init__.py
2.8 kB
tab.py
15.0 kB
tests
__init__.py
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data
Library-clusterset-N.validated.tsv
2.8 kB
annotations_subsample.json
34.6 kB
annotations_subsample.tab
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bad_input_file.cfg
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blat_input.fa
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blat_output.pslx
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breakdancer_output.txt
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breakseq.vcf
25.9 kB
build.cfg
3.7 kB
bwa_pipeline_config.cfg
2.2 kB
chimerascan_output.bedpe
12.0 kB
clean_pipeline_config.cfg
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clinvar_short_test.vcf
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clustering_input.tab
526 Bytes
cnvnator.tab
752 Bytes
cytoBand.txt
30.9 kB
defuse_output.tsv
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delly_events.vcf
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example_genes.fa
1.8 MB
example_genes.json
307.4 kB
large_assembly.txt
1.3 MB
long_filter_assembly.txt
81.2 kB
manta_events.vcf
10.1 kB
mavis_summary_all_mock-A36971_mock-A47933.tab
48.1 kB
mini_mock_reads_for_events.sorted.bam
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mini_mock_reads_for_events.sorted.bam.bai
264 Bytes
mini_mock_sv_events.svmerge.tsv
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missing_reference.cfg
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mock_annotations.json
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mock_dgv_annotation.txt
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mock_masking.tab
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mock_pairing_input.tab
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mock_reads_for_events.sorted.bam
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mock_reads_for_events.sorted.bam.bai
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mock_reference_annotations.full.tsv
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mock_reference_annotations.json
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mock_reference_annotations.tsv
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mock_reference_genome.2bit
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mock_reference_genome.fa
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mock_reference_genome.fa.amb
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mock_reference_genome.fa.ann
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mock_reference_genome.fa.bwt
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mock_reference_genome.fa.pac
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mock_reference_genome.fa.sa
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mock_sv_events.tsv
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mock_trans_reads_for_events.sorted.bam
932.4 kB
mock_trans_reads_for_events.sorted.bam.bai
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mock_trans_sv_events.tsv
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mutect.vcf
48.2 kB
no_opt_pipeline.cfg
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pairing_annotations.tab
23.4 kB
pairing_reference_annotations_file.tab
464 Bytes
pairing_sequences.fa
9.7 kB
pindel_events.vcf
9.3 kB
pipeline_config.cfg
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reference_from_env.cfg
316 Bytes
similar_contigs.txt
76.6 kB
strelka.vcf
36.4 kB
torque_build.cfg
7.3 kB
transabyss_events.tab
5.2 kB
transabyss_indels_output.tab
3.8 kB
end_to_end
__init__.py
514 Bytes
test_config.py
6.6 kB
test_convert.py
4.9 kB
test_full_pipeline.py
16.6 kB
test_help.py
3.9 kB
test_overlay.py
7.2 kB
test_pairing.py
1.3 kB
test_ref_alt_count.py
4.4 kB
integration
__init__.py
9.9 kB
config.py
0 Bytes
schedule
__init__.py
0 Bytes
test_pipeline.py
4.8 kB
test_sge.py
25.1 kB
test_slurm.py
45.6 kB
test_torque.py
17.1 kB
test_align.py
33.9 kB
test_annotate.py
75.6 kB
test_annotate_examples.py
9.1 kB
test_annotate_fileio.py
1.6 kB
test_args.py
10.8 kB
test_assemble.py
68.7 kB
test_bam.py
20.2 kB
test_bam_cigar.py
26.3 kB
test_blat.py
13.5 kB
test_breakpoint.py
9.9 kB
test_checker.py
5.7 kB
test_cluster.py
6.9 kB
test_config.py
1.8 kB
test_illustrate.py
24.5 kB
test_mains.py
4.4 kB
test_pairing.py
17.5 kB
test_splicing.py
12.9 kB
test_validate.py
34.0 kB
test_validate_call.py
67.2 kB
test_validate_evidence.py
25.3 kB
unit
__init__.py
0 Bytes
data
calc_orf_test_sequence.fa
4.2 MB
reference_sequences.fa
1.1 MB
test_assembly_sequences.txt
60.4 kB
mock.py
1.2 kB
test_annotate.py
26.5 kB
test_assemble.py
7.3 kB
test_bam.py
13.0 kB
test_blat.py
3.0 kB
test_breakpoint.py
18.7 kB
test_call_indels.py
12.7 kB
test_cluster.py
921 Bytes
test_config.py
1.9 kB
test_constants.py
4.5 kB
test_illustrate.py
1.1 kB
test_interval.py
14.4 kB
test_summary.py
6.2 kB
test_tab.py
10.0 kB
test_tool.py
43.4 kB
test_util.py
16.6 kB
test_validate.py
2.1 kB
util.py
136 Bytes
tools
TSV.pm
6.4 kB
calculate_ref_alt_counts.py
10.4 kB
find_repeats.py
3.1 kB
generate_ensembl_json.py
19.6 kB
get_hg19_reference_files.sh
1.6 kB