MANIFEST.in
README.rst
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/call.py
kevlar/count.py
kevlar/counting.py
kevlar/dump.py
kevlar/filter.py
kevlar/localize.py
kevlar/mutate.py
kevlar/novel.py
kevlar/overlap.py
kevlar/partition.py
kevlar/readgraph.py
kevlar/reaugment.py
kevlar/seqio.py
kevlar/simplex.py
kevlar/sketch.py
kevlar/timer.py
kevlar/variantset.py
kevlar/cli/__init__.py
kevlar/cli/alac.py
kevlar/cli/assemble.py
kevlar/cli/call.py
kevlar/cli/count.py
kevlar/cli/dump.py
kevlar/cli/filter.py
kevlar/cli/localize.py
kevlar/cli/mutate.py
kevlar/cli/novel.py
kevlar/cli/partition.py
kevlar/cli/reaugment.py
kevlar/cli/simplex.py
kevlar/tests/__init__.py
kevlar/tests/test_alac.py
kevlar/tests/test_assemble.py
kevlar/tests/test_call.py
kevlar/tests/test_cli.py
kevlar/tests/test_count.py
kevlar/tests/test_dump.py
kevlar/tests/test_filter.py
kevlar/tests/test_localize.py
kevlar/tests/test_mutate.py
kevlar/tests/test_novel.py
kevlar/tests/test_overlap.py
kevlar/tests/test_partition.py
kevlar/tests/test_reaugment.py
kevlar/tests/test_seqio.py
kevlar/tests/test_simplex.py
kevlar/tests/test_sketch.py
kevlar/tests/test_variant_set.py
kevlar/tests/data/AluContigs.augfastq
kevlar/tests/data/asmbl-no-edges.augfastq.gz
kevlar/tests/data/chr19.indel.fa
kevlar/tests/data/chr19.order2.rand.100k.fa
kevlar/tests/data/collect.alpha.txt
kevlar/tests/data/collect.beta.1.txt
kevlar/tests/data/collect.beta.2.txt
kevlar/tests/data/collect.gamma.txt
kevlar/tests/data/dup.augfastq
kevlar/tests/data/dupl-part-2reads.augfastq.gz
kevlar/tests/data/dupl-part.augfastq.gz
kevlar/tests/data/example1.augfastq
kevlar/tests/data/example2.augfastq
kevlar/tests/data/example2.augfastq.gz
kevlar/tests/data/human-random-pico.fa.gz
kevlar/tests/data/human-random-pico.fa.gz.amb
kevlar/tests/data/human-random-pico.fa.gz.ann
kevlar/tests/data/human-random-pico.fa.gz.bwt
kevlar/tests/data/human-random-pico.fa.gz.pac
kevlar/tests/data/human-random-pico.fa.gz.sa
kevlar/tests/data/localize-contig-bad.fa
kevlar/tests/data/localize-contig.fa
kevlar/tests/data/localize-refr.fa
kevlar/tests/data/localize-refr.fa.amb
kevlar/tests/data/localize-refr.fa.ann
kevlar/tests/data/localize-refr.fa.bwt
kevlar/tests/data/localize-refr.fa.pac
kevlar/tests/data/localize-refr.fa.sa
kevlar/tests/data/make-bogus-genome.sh
kevlar/tests/data/make-bogus-reads.py
kevlar/tests/data/make-indel-reads.py
kevlar/tests/data/make-trio-data.sh
kevlar/tests/data/mut-genome.fa
kevlar/tests/data/mut-genome.txt
kevlar/tests/data/mutate-indel-chr19.py
kevlar/tests/data/mutate-indel.py
kevlar/tests/data/mutate1.py
kevlar/tests/data/mutate3.py
kevlar/tests/data/muts-w.txt
kevlar/tests/data/muts-x.txt
kevlar/tests/data/muts-y.tsv
kevlar/tests/data/muts-z.csv
kevlar/tests/data/nopair.sam
kevlar/tests/data/phony-deletion-01.contig.fa
kevlar/tests/data/phony-deletion-01.gdna.fa
kevlar/tests/data/phony-deletion-02.contig.fa
kevlar/tests/data/phony-deletion-02.gdna.fa
kevlar/tests/data/phony-insertion-01.contig.fa
kevlar/tests/data/phony-insertion-01.gdna.fa
kevlar/tests/data/phony-insertion-02.contig.fa
kevlar/tests/data/phony-insertion-02.gdna.fa
kevlar/tests/data/phony-snv-01.contig.fa
kevlar/tests/data/phony-snv-01.gdna.fa
kevlar/tests/data/phony-snv-02.contig.fa
kevlar/tests/data/phony-snv-02.gdna.fa
kevlar/tests/data/pico-2-asmbl.fa
kevlar/tests/data/pico-2-refr.fa
kevlar/tests/data/pico-4.augfastq.gz
kevlar/tests/data/pico-7-asmbl.fa
kevlar/tests/data/pico-7-refr.fa
kevlar/tests/data/pico-filtered.fq.gz
kevlar/tests/data/pico5.contig.augfasta
kevlar/tests/data/pico5.gdna.fa
kevlar/tests/data/pico7.contig.augfasta
kevlar/tests/data/pico7.gdna.fa
kevlar/tests/data/pico9.contig.augfasta
kevlar/tests/data/pico9.gdna.fa
kevlar/tests/data/reads2chain.fq.gz
kevlar/tests/data/reaugment.augfastq
kevlar/tests/data/reaugment.fq
kevlar/tests/data/reaugment.out
kevlar/tests/data/screen-case.fa
kevlar/tests/data/screen-ctrl.fa
kevlar/tests/data/simple-case.mut.txt
kevlar/tests/data/simple-ctrl1.mut.txt
kevlar/tests/data/simple-ctrl2.mut.txt
kevlar/tests/data/simple-genome-case-reads.fa.gz
kevlar/tests/data/simple-genome-case.fa
kevlar/tests/data/simple-genome-ctrl1-reads.fa.gz
kevlar/tests/data/simple-genome-ctrl1.fa
kevlar/tests/data/simple-genome-ctrl2-reads.fa.gz
kevlar/tests/data/simple-genome-ctrl2.fa
kevlar/tests/data/simple-genome.fa
kevlar/tests/data/smallseq.augfasta
kevlar/tests/data/smallseq.fa.gz
kevlar/tests/data/smallseq.fq
kevlar/tests/data/ssc106.contig.augfasta
kevlar/tests/data/ssc106.gdna.fa
kevlar/tests/data/ssc107.contig.augfasta.gz
kevlar/tests/data/ssc107.gdna.fa.gz
kevlar/tests/data/ssc124.contig.augfasta.gz
kevlar/tests/data/ssc124.gdna.fa.gz
kevlar/tests/data/ssc218.contig.augfasta
kevlar/tests/data/ssc218.gdna.fa
kevlar/tests/data/ssc223.contig.augfasta
kevlar/tests/data/ssc223.gdna.fa
kevlar/tests/data/ssc62.contig.augfasta
kevlar/tests/data/ssc62.gdna.fa
kevlar/tests/data/test.countgraph
kevlar/tests/data/test.counttable
kevlar/tests/data/test.nodegraph
kevlar/tests/data/test.nodetable
kevlar/tests/data/test.notasketchtype
kevlar/tests/data/test.smallcountgraph
kevlar/tests/data/test.smallcounttable
kevlar/tests/data/topartition.augfastq
kevlar/tests/data/var1.gdna.fa
kevlar/tests/data/var1.reads.augfastq
kevlar/tests/data/var1.round2.augfastq
kevlar/tests/data/bogus-genome/contam1.fa
kevlar/tests/data/bogus-genome/mask-chr1.fa
kevlar/tests/data/bogus-genome/mask-chr2.fa
kevlar/tests/data/bogus-genome/mask.nt
kevlar/tests/data/bogus-genome/reads-indels.bam
kevlar/tests/data/bogus-genome/reads.bam
kevlar/tests/data/bogus-genome/refr.fa
kevlar/tests/data/bogus-genome/refr.fa.amb
kevlar/tests/data/bogus-genome/refr.fa.ann
kevlar/tests/data/bogus-genome/refr.fa.bwt
kevlar/tests/data/bogus-genome/refr.fa.pac
kevlar/tests/data/bogus-genome/refr.fa.sa
kevlar/tests/data/bogus-genome/seq-pool-1indel.fa
kevlar/tests/data/bogus-genome/seq-pool-1snp-contam.fa
kevlar/tests/data/bogus-genome/seq-pool-1snp.fa
kevlar/tests/data/bogus-genome/seq-pool-3snps.fa
kevlar/tests/data/edgeless/cc139.afq.gz
kevlar/tests/data/edgeless/cc27.afq.gz
kevlar/tests/data/edgeless/cc278.afq.gz
kevlar/tests/data/edgeless/cc327.afq.gz
kevlar/tests/data/edgeless/cc379.afq.gz
kevlar/tests/data/fml/cc110.afq.gz
kevlar/tests/data/fml/cc206.afq.gz
kevlar/tests/data/fml/cc231.afq.gz
kevlar/tests/data/fml/cc322.afq.gz
kevlar/tests/data/fml/cc58.afq.gz
kevlar/tests/data/pico-var/cc10.afq.gz
kevlar/tests/data/pico-var/cc2.afq.gz
kevlar/tests/data/pico-var/cc3.afq.gz
kevlar/tests/data/pico-var/cc5.afq.gz
kevlar/tests/data/pico-var/cc6.afq.gz
kevlar/tests/data/pico-var/cc7.afq.gz
kevlar/tests/data/pico-var/cc8.afq.gz
kevlar/tests/data/pico-var/cc9.afq.gz
kevlar/tests/data/trio1/case1.fq
kevlar/tests/data/trio1/case2.fq
kevlar/tests/data/trio1/case3.fq
kevlar/tests/data/trio1/case4.fq
kevlar/tests/data/trio1/case5.fq
kevlar/tests/data/trio1/case6.fq
kevlar/tests/data/trio1/case6b.fq
kevlar/tests/data/trio1/case7.fq
kevlar/tests/data/trio1/ctrl1.fq
kevlar/tests/data/trio1/ctrl2.fq
kevlar/tests/data/trio1/ctrl3.fq
kevlar/tests/data/trio1/ctrl4.fq
kevlar/tests/data/trio1/ctrl5.fq
kevlar/tests/data/trio1/ctrl6.fq
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
src/align.c
third-party/README.md
third-party/fermi-lite/.gitignore
third-party/fermi-lite/FERMILITE_VERSION
third-party/fermi-lite/LICENSE.txt
third-party/fermi-lite/Makefile
third-party/fermi-lite/README.md
third-party/fermi-lite/bfc.c
third-party/fermi-lite/bseq.c
third-party/fermi-lite/bubble.c
third-party/fermi-lite/fml.h
third-party/fermi-lite/htab.c
third-party/fermi-lite/htab.h
third-party/fermi-lite/internal.h
third-party/fermi-lite/khash.h
third-party/fermi-lite/kmer.h
third-party/fermi-lite/kseq.h
third-party/fermi-lite/ksort.h
third-party/fermi-lite/kstring.h
third-party/fermi-lite/ksw.c
third-party/fermi-lite/ksw.h
third-party/fermi-lite/kthread.c
third-party/fermi-lite/kvec.h
third-party/fermi-lite/mag.c
third-party/fermi-lite/mag.h
third-party/fermi-lite/misc.c
third-party/fermi-lite/mrope.c
third-party/fermi-lite/mrope.h
third-party/fermi-lite/rld0.c
third-party/fermi-lite/rld0.h
third-party/fermi-lite/rle.c
third-party/fermi-lite/rle.h
third-party/fermi-lite/rope.c
third-party/fermi-lite/rope.h
third-party/fermi-lite/unitig.c
third-party/fermi-lite/test/MT-simu.fq.gz
third-party/ksw2/KSW2_VERSION
third-party/ksw2/README.md
third-party/ksw2/ksw2.h
third-party/ksw2/ksw2_extz.c