LICENSE
MANIFEST.in
README.md
setup.cfg
setup.py
docs/development.md
docs/extra.css
docs/glossary.md
docs/hooks.py
docs/index.md
docs/background/citations.md
docs/background/theory.md
docs/configuration/general.md
docs/configuration/performance.md
docs/configuration/pipeline.md
docs/configuration/settings.md
docs/images/ENSG00000139687_RB1_overlay.png
docs/images/Fusion-ext.gpl
docs/images/GIMAP4_IL7_fusion.svg
docs/images/UBE2V2_GIMAP4_disruptive_fusion.svg
docs/images/acronym.svg
docs/images/annotation_case_dup.svg
docs/images/annotation_case_indel.svg
docs/images/annotation_case_inversion.svg
docs/images/annotation_model.svg
docs/images/annotations_summary.svg
docs/images/breakpoint_comparison_model.svg
docs/images/breakpoint_prediction_exonic.svg
docs/images/call_breakpoint_by_flanking_reads.svg
docs/images/classification_tree.svg
docs/images/colo829_tumour_annotation_resource_req.png
docs/images/colo829_tumour_validation_resource_req.png
docs/images/compatible_flanking_pairs.svg
docs/images/example_figure.svg
docs/images/feature_levels.svg
docs/images/flanking_pairs_fragment_sizes_deletion.svg
docs/images/fragment_sizes_histogram.svg
docs/images/get_app-24px.svg
docs/images/icon.png
docs/images/pipeline_dependency_graph.svg
docs/images/pipeline_options.svg
docs/images/read_evidence.svg
docs/images/read_pair_definitions.svg
docs/images/read_pairs_deletion.svg
docs/images/read_pairs_duplication.svg
docs/images/read_pairs_insertion.svg
docs/images/read_pairs_inversion_LL.svg
docs/images/read_pairs_inversion_RR.svg
docs/images/read_pairs_translocated_inversion_LL.svg
docs/images/read_pairs_translocated_inversion_RR.svg
docs/images/read_pairs_translocation_LR.svg
docs/images/read_pairs_translocation_RL.svg
docs/images/read_pairs_vs_contigs_evidence.svg
docs/images/splicing_model.svg
docs/images/splicing_pattern_default.svg
docs/images/splicing_pattern_multiple_acceptors.svg
docs/images/splicing_pattern_multiple_donors.svg
docs/inputs/reference.md
docs/inputs/standard.md
docs/inputs/support.md
docs/outputs/columns.md
docs/outputs/illustrations.md
docs/outputs/index.md
docs/package/mavis/annotate/index.md
docs/package/mavis/cluster/index.md
docs/package/mavis/pairing/index.md
docs/package/mavis/summary/index.md
docs/package/mavis/validate/index.md
docs/tutorials/full.md
docs/tutorials/mini.md
mavis/__init__.py
mavis/align.py
mavis/assemble.py
mavis/blat.py
mavis/breakpoint.py
mavis/config.py
mavis/constants.py
mavis/error.py
mavis/interval.py
mavis/main.py
mavis/util.py
mavis.egg-info/PKG-INFO
mavis.egg-info/SOURCES.txt
mavis.egg-info/dependency_links.txt
mavis.egg-info/entry_points.txt
mavis.egg-info/requires.txt
mavis.egg-info/top_level.txt
mavis/annotate/__init__.py
mavis/annotate/base.py
mavis/annotate/constants.py
mavis/annotate/file_io.py
mavis/annotate/fusion.py
mavis/annotate/genomic.py
mavis/annotate/main.py
mavis/annotate/protein.py
mavis/annotate/splicing.py
mavis/annotate/variant.py
mavis/bam/__init__.py
mavis/bam/cache.py
mavis/bam/cigar.py
mavis/bam/read.py
mavis/bam/stats.py
mavis/cluster/__init__.py
mavis/cluster/cluster.py
mavis/cluster/constants.py
mavis/cluster/main.py
mavis/illustrate/__init__.py
mavis/illustrate/constants.py
mavis/illustrate/diagram.py
mavis/illustrate/elements.py
mavis/illustrate/scatter.py
mavis/illustrate/util.py
mavis/pairing/__init__.py
mavis/pairing/constants.py
mavis/pairing/main.py
mavis/pairing/pairing.py
mavis/schedule/__init__.py
mavis/schedule/constants.py
mavis/schedule/job.py
mavis/schedule/local.py
mavis/schedule/pipeline.py
mavis/schedule/scheduler.py
mavis/summary/__init__.py
mavis/summary/constants.py
mavis/summary/main.py
mavis/summary/summary.py
mavis/tools/__init__.py
mavis/tools/arriba.py
mavis/tools/breakdancer.py
mavis/tools/chimerascan.py
mavis/tools/cnvnator.py
mavis/tools/constants.py
mavis/tools/starfusion.py
mavis/tools/transabyss.py
mavis/tools/vcf.py
mavis/validate/__init__.py
mavis/validate/base.py
mavis/validate/call.py
mavis/validate/constants.py
mavis/validate/evidence.py
mavis/validate/main.py
tab/__init__.py
tab/tab.py
tests/__init__.py
tests/util.py
tests/end_to_end/__init__.py
tests/end_to_end/test_config.py
tests/end_to_end/test_convert.py
tests/end_to_end/test_full_pipeline.py
tests/end_to_end/test_help.py
tests/end_to_end/test_overlay.py
tests/end_to_end/test_pairing.py
tests/end_to_end/test_ref_alt_count.py
tests/integration/__init__.py
tests/integration/config.py
tests/integration/test_align.py
tests/integration/test_annotate.py
tests/integration/test_annotate_examples.py
tests/integration/test_annotate_fileio.py
tests/integration/test_args.py
tests/integration/test_assemble.py
tests/integration/test_bam.py
tests/integration/test_bam_cigar.py
tests/integration/test_blat.py
tests/integration/test_breakpoint.py
tests/integration/test_checker.py
tests/integration/test_cluster.py
tests/integration/test_config.py
tests/integration/test_illustrate.py
tests/integration/test_mains.py
tests/integration/test_pairing.py
tests/integration/test_splicing.py
tests/integration/test_validate.py
tests/integration/test_validate_call.py
tests/integration/test_validate_evidence.py
tests/integration/schedule/__init__.py
tests/integration/schedule/test_pipeline.py
tests/integration/schedule/test_sge.py
tests/integration/schedule/test_slurm.py
tests/integration/schedule/test_torque.py
tests/unit/__init__.py
tests/unit/mock.py
tests/unit/test_annotate.py
tests/unit/test_assemble.py
tests/unit/test_bam.py
tests/unit/test_blat.py
tests/unit/test_breakpoint.py
tests/unit/test_call_indels.py
tests/unit/test_cluster.py
tests/unit/test_config.py
tests/unit/test_constants.py
tests/unit/test_illustrate.py
tests/unit/test_interval.py
tests/unit/test_summary.py
tests/unit/test_tab.py
tests/unit/test_tool.py
tests/unit/test_util.py
tests/unit/test_validate.py
tests/unit/data/calc_orf_test_sequence.fa
tests/unit/data/reference_sequences.fa
tests/unit/data/test_assembly_sequences.txt
tools/TSV.pm
tools/calculate_ref_alt_counts.py
tools/find_repeats.py
tools/generate_ensembl_json.py