LICENSE.txt
MANIFEST.in
README.md
setup.cfg
setup.py
docs/Makefile
docs/preprocess.py
docs/source/about.rst
docs/source/citations.rst
docs/source/conf.py
docs/source/configuration.rst
docs/source/development.rst
docs/source/glossary.rst
docs/source/illustrations.rst
docs/source/index.rst
docs/source/mavis.annotate.rst
docs/source/mavis.bam.rst
docs/source/mavis.cluster.rst
docs/source/mavis.illustrate.rst
docs/source/mavis.pairing.rst
docs/source/mavis.schedule.rst
docs/source/mavis.summary.rst
docs/source/mavis.validate.rst
docs/source/mavis_input.rst
docs/source/package.rst
docs/source/performance.rst
docs/source/pipeline.rst
docs/source/reference.rst
docs/source/supported_dependencies.rst
docs/source/theory.rst
docs/source/tutorial.rst
docs/source/_static/ENSG00000139687_RB1_overlay.png
docs/source/_static/Fusion-ext.gpl
docs/source/_static/GIMAP4_IL7_fusion.svg
docs/source/_static/Ic_cloud_download_48px.svg
docs/source/_static/UBE2V2_GIMAP4_disruptive_fusion.svg
docs/source/_static/acronym.svg
docs/source/_static/annotation_case_dup.svg
docs/source/_static/annotation_case_indel.svg
docs/source/_static/annotation_case_inversion.svg
docs/source/_static/annotation_model.svg
docs/source/_static/annotations_summary.svg
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docs/source/_static/classification_tree.svg
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docs/source/_static/custom.css
docs/source/_static/example_figure.svg
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docs/source/_static/fragment_sizes_histogram.svg
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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/tools.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/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/test_style.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/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
tools/TSV.pm
tools/find_repeats.py
tools/generate_ensembl_json.pl
tools/test_input_file.py