MANIFEST.in
README.md
setup.cfg
setup.py
versioneer.py
biokevlar.egg-info/PKG-INFO
biokevlar.egg-info/SOURCES.txt
biokevlar.egg-info/dependency_links.txt
biokevlar.egg-info/entry_points.txt
biokevlar.egg-info/requires.txt
biokevlar.egg-info/top_level.txt
biokevlar.egg-info/zip-safe
inc/align.h
kevlar/__init__.py
kevlar/__main__.py
kevlar/_version.py
kevlar/alac.py
kevlar/alignment.c
kevlar/assemble.py
kevlar/assembly.c
kevlar/augment.py
kevlar/call.py
kevlar/cigar.py
kevlar/count.py
kevlar/dist.py
kevlar/evaluate.py
kevlar/filter.py
kevlar/gentrio.py
kevlar/intervalforest.py
kevlar/localize.py
kevlar/mutablestring.py
kevlar/mutate.py
kevlar/novel.py
kevlar/partition.py
kevlar/progress.py
kevlar/readgraph.py
kevlar/readpair.py
kevlar/reference.py
kevlar/seqio.py
kevlar/sequence.c
kevlar/simlike.py
kevlar/sketch.py
kevlar/split.py
kevlar/timer.py
kevlar/unband.py
kevlar/varfilter.py
kevlar/varmap.py
kevlar/vcf.py
kevlar/cli/__init__.py
kevlar/cli/alac.py
kevlar/cli/assemble.py
kevlar/cli/augment.py
kevlar/cli/call.py
kevlar/cli/count.py
kevlar/cli/dist.py
kevlar/cli/filter.py
kevlar/cli/gentrio.py
kevlar/cli/localize.py
kevlar/cli/mutate.py
kevlar/cli/novel.py
kevlar/cli/partition.py
kevlar/cli/simlike.py
kevlar/cli/split.py
kevlar/cli/unband.py
kevlar/cli/varfilter.py
kevlar/sandbox/compact.py
kevlar/sandbox/get-partitions.py
kevlar/sandbox/subsketch.py
kevlar/tests/__init__.py
kevlar/tests/test_alac.py
kevlar/tests/test_assemble.py
kevlar/tests/test_augment.py
kevlar/tests/test_call.py
kevlar/tests/test_cigar.py
kevlar/tests/test_cli.py
kevlar/tests/test_count.py
kevlar/tests/test_dist.py
kevlar/tests/test_evaluate.py
kevlar/tests/test_filter.py
kevlar/tests/test_gentrio.py
kevlar/tests/test_localize.py
kevlar/tests/test_mutablestring.py
kevlar/tests/test_mutate.py
kevlar/tests/test_novel.py
kevlar/tests/test_partition.py
kevlar/tests/test_progress.py
kevlar/tests/test_readgraph.py
kevlar/tests/test_readpair.py
kevlar/tests/test_reference.py
kevlar/tests/test_seqio.py
kevlar/tests/test_simlike.py
kevlar/tests/test_sketch.py
kevlar/tests/test_split.py
kevlar/tests/test_timer.py
kevlar/tests/test_unband.py
kevlar/tests/test_varfilter.py
kevlar/tests/test_varmap.py
kevlar/tests/test_vcf.py
kevlar/tests/data/.gitignore
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kevlar/tests/data/make-indel-reads.py
kevlar/tests/data/make-trio-data.sh
kevlar/tests/data/maxdiff-contig.augfasta
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kevlar/tests/data/mutate1.py
kevlar/tests/data/mutate3.py
kevlar/tests/data/muts-w.txt
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kevlar/tests/data/trio1/ctrl7.fq
kevlar/tests/data/trio1/ctrl8.fq
kevlar/tests/data/trio1/novel_1_1,2.txt
kevlar/tests/data/trio1/novel_1_1,2_batch3.txt
kevlar/tests/data/trio1/novel_1_1,2_batch4.txt
kevlar/tests/data/trio1/novel_1_1,2_batch5.txt
kevlar/tests/data/trio1/novel_1_1,2_batch7.txt
kevlar/tests/data/trio1/novel_1_1,2_batch8.txt
kevlar/tests/data/trio1/novel_2_1,2.txt
kevlar/tests/data/trio1/novel_3_1,2.txt
kevlar/tests/data/trio1/novel_4_1,2.txt
kevlar/tests/data/trio1/novel_5_3,4.txt
kevlar/tests/data/trio1/novel_6_5,6.txt
kevlar/tests/data/trio2/case1.fq.gz
kevlar/tests/data/trio2/ctrl1.fq.gz
kevlar/tests/data/trio2/ctrl2.fq.gz
kevlar/workflows/bam-preproc/README.md
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kevlar/workflows/bam-preproc/config.json
kevlar/workflows/mark-I/README.md
kevlar/workflows/mark-I/Snakefile
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src/align.c
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third-party/ksw2/KSW2_VERSION
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