COPYING
ChangeLog
INSTALL
INSTALL.html
LICENSE.txt
MANIFEST.in
README.txt
setup.py
css/screen.css
lib/MiModD/__init__.py
lib/MiModD/__main__.py
lib/MiModD/anno_weblinks.py
lib/MiModD/auxparsers.py
lib/MiModD/bioobj_base.py
lib/MiModD/cfg.py
lib/MiModD/cloudmap.py
lib/MiModD/config.py
lib/MiModD/convert.py
lib/MiModD/decox.py
lib/MiModD/deletion_calling.py
lib/MiModD/enablegalaxy.py
lib/MiModD/fasta.py
lib/MiModD/fileinfo.py
lib/MiModD/fisher.py
lib/MiModD/index.py
lib/MiModD/iterx.py
lib/MiModD/pybcftools.py
lib/MiModD/pysamtools.py
lib/MiModD/pyvcf.py
lib/MiModD/samheader.py
lib/MiModD/sanitize.py
lib/MiModD/snap.py
lib/MiModD/tmpfiles.py
lib/MiModD/upgrade.py
lib/MiModD/variant_annotation.py
lib/MiModD/variant_calling.py
lib/MiModD/vcf_filter.py
lib/MiModD.egg-info/PKG-INFO
lib/MiModD.egg-info/SOURCES.txt
lib/MiModD.egg-info/dependency_links.txt
lib/MiModD.egg-info/top_level.txt
lib/MiModD/galaxy_data/mimodd_tool_conf.xml
lib/MiModD/galaxy_data/mimodd/annotate_variants.xml
lib/MiModD/galaxy_data/mimodd/bamsort.xml
lib/MiModD/galaxy_data/mimodd/cloudmap.xml
lib/MiModD/galaxy_data/mimodd/convert.xml
lib/MiModD/galaxy_data/mimodd/covstats.xml
lib/MiModD/galaxy_data/mimodd/deletion_predictor.xml
lib/MiModD/galaxy_data/mimodd/fileinfo.xml
lib/MiModD/galaxy_data/mimodd/reheader.xml
lib/MiModD/galaxy_data/mimodd/sam_header.xml
lib/MiModD/galaxy_data/mimodd/snap_caller.xml
lib/MiModD/galaxy_data/mimodd/snp_caller_caller.xml
lib/MiModD/galaxy_data/mimodd/snpeff_genomes.xml
lib/MiModD/galaxy_data/mimodd/varextract.xml
lib/MiModD/galaxy_data/mimodd/vcf_filter.xml
pysam/bcftools-1.x/AUTHORS
pysam/bcftools-1.x/HMM.c
pysam/bcftools-1.x/HMM.h
pysam/bcftools-1.x/INSTALL
pysam/bcftools-1.x/LICENSE
pysam/bcftools-1.x/Makefile
pysam/bcftools-1.x/README
pysam/bcftools-1.x/bcftools.h
pysam/bcftools-1.x/call.h
pysam/bcftools-1.x/ccall.c
pysam/bcftools-1.x/consensus.c
pysam/bcftools-1.x/convert.c
pysam/bcftools-1.x/convert.h
pysam/bcftools-1.x/em.c
pysam/bcftools-1.x/filter.c
pysam/bcftools-1.x/filter.h
pysam/bcftools-1.x/gvcf.c
pysam/bcftools-1.x/khash_str2str.h
pysam/bcftools-1.x/kmin.c
pysam/bcftools-1.x/kmin.h
pysam/bcftools-1.x/main.c
pysam/bcftools-1.x/mcall.c
pysam/bcftools-1.x/ploidy.c
pysam/bcftools-1.x/ploidy.h
pysam/bcftools-1.x/plot-vcfstats
pysam/bcftools-1.x/polysomy.c
pysam/bcftools-1.x/prob1.c
pysam/bcftools-1.x/prob1.h
pysam/bcftools-1.x/rbuf.h
pysam/bcftools-1.x/reheader.c
pysam/bcftools-1.x/tabix.c
pysam/bcftools-1.x/tsv2vcf.c
pysam/bcftools-1.x/tsv2vcf.h
pysam/bcftools-1.x/vcfannotate.c
pysam/bcftools-1.x/vcfcall.c
pysam/bcftools-1.x/vcfcnv.c
pysam/bcftools-1.x/vcfconcat.c
pysam/bcftools-1.x/vcfconvert.c
pysam/bcftools-1.x/vcffilter.c
pysam/bcftools-1.x/vcfgtcheck.c
pysam/bcftools-1.x/vcfindex.c
pysam/bcftools-1.x/vcfisec.c
pysam/bcftools-1.x/vcfmerge.c
pysam/bcftools-1.x/vcfnorm.c
pysam/bcftools-1.x/vcfplugin.c
pysam/bcftools-1.x/vcfquery.c
pysam/bcftools-1.x/vcfroh.c
pysam/bcftools-1.x/vcfsom.c
pysam/bcftools-1.x/vcfstats.c
pysam/bcftools-1.x/vcfutils.pl
pysam/bcftools-1.x/vcfview.c
pysam/bcftools-1.x/vcmp.c
pysam/bcftools-1.x/vcmp.h
pysam/bcftools-1.x/version.c
pysam/bcftools-1.x/plugins/counts.c
pysam/bcftools-1.x/plugins/dosage.c
pysam/bcftools-1.x/plugins/fill-AN-AC.c
pysam/bcftools-1.x/plugins/fixploidy.c
pysam/bcftools-1.x/plugins/fixploidy.mk
pysam/bcftools-1.x/plugins/frameshifts.c
pysam/bcftools-1.x/plugins/missing2ref.c
pysam/bcftools-1.x/plugins/tag2tag.c
pysam/bcftools-1.x/plugins/vcf2sex.c
pysam/bcftools-1.x/plugins/vcf2sex.mk
pysam/htslib-1.x/INSTALL
pysam/htslib-1.x/LICENSE
pysam/htslib-1.x/Makefile
pysam/htslib-1.x/NEWS
pysam/htslib-1.x/README
pysam/htslib-1.x/bgzf.c
pysam/htslib-1.x/bgzip.c
pysam/htslib-1.x/config.mk.in
pysam/htslib-1.x/configure
pysam/htslib-1.x/configure.ac
pysam/htslib-1.x/faidx.5
pysam/htslib-1.x/faidx.c
pysam/htslib-1.x/hfile.c
pysam/htslib-1.x/hfile_internal.h
pysam/htslib-1.x/hfile_irods.c
pysam/htslib-1.x/hfile_net.c
pysam/htslib-1.x/hts.c
pysam/htslib-1.x/htsfile.1
pysam/htslib-1.x/htsfile.c
pysam/htslib-1.x/htslib.mk
pysam/htslib-1.x/htslib.pc.in
pysam/htslib-1.x/htslib_vars.mk
pysam/htslib-1.x/kfunc.c
pysam/htslib-1.x/knetfile.c
pysam/htslib-1.x/kstring.c
pysam/htslib-1.x/regidx.c
pysam/htslib-1.x/sam.5
pysam/htslib-1.x/sam.c
pysam/htslib-1.x/synced_bcf_reader.c
pysam/htslib-1.x/tabix.1
pysam/htslib-1.x/tabix.c
pysam/htslib-1.x/tbx.c
pysam/htslib-1.x/vcf.5
pysam/htslib-1.x/vcf.c
pysam/htslib-1.x/vcf.c.orig
pysam/htslib-1.x/vcf_sweep.c
pysam/htslib-1.x/vcfutils.c
pysam/htslib-1.x/cram/cram.h
pysam/htslib-1.x/cram/cram_codecs.c
pysam/htslib-1.x/cram/cram_codecs.h
pysam/htslib-1.x/cram/cram_decode.c
pysam/htslib-1.x/cram/cram_decode.h
pysam/htslib-1.x/cram/cram_encode.c
pysam/htslib-1.x/cram/cram_encode.h
pysam/htslib-1.x/cram/cram_index.c
pysam/htslib-1.x/cram/cram_index.h
pysam/htslib-1.x/cram/cram_io.c
pysam/htslib-1.x/cram/cram_io.h
pysam/htslib-1.x/cram/cram_samtools.c
pysam/htslib-1.x/cram/cram_samtools.h
pysam/htslib-1.x/cram/cram_stats.c
pysam/htslib-1.x/cram/cram_stats.h
pysam/htslib-1.x/cram/cram_structs.h
pysam/htslib-1.x/cram/files.c
pysam/htslib-1.x/cram/mFILE.c
pysam/htslib-1.x/cram/mFILE.h
pysam/htslib-1.x/cram/md5.c
pysam/htslib-1.x/cram/md5.h
pysam/htslib-1.x/cram/misc.h
pysam/htslib-1.x/cram/open_trace_file.c
pysam/htslib-1.x/cram/open_trace_file.h
pysam/htslib-1.x/cram/os.h
pysam/htslib-1.x/cram/pooled_alloc.c
pysam/htslib-1.x/cram/pooled_alloc.h
pysam/htslib-1.x/cram/rANS_byte.h
pysam/htslib-1.x/cram/rANS_static.c
pysam/htslib-1.x/cram/rANS_static.h
pysam/htslib-1.x/cram/sam_header.c
pysam/htslib-1.x/cram/sam_header.h
pysam/htslib-1.x/cram/string_alloc.c
pysam/htslib-1.x/cram/string_alloc.h
pysam/htslib-1.x/cram/thread_pool.c
pysam/htslib-1.x/cram/thread_pool.h
pysam/htslib-1.x/cram/vlen.c
pysam/htslib-1.x/cram/vlen.h
pysam/htslib-1.x/cram/zfio.c
pysam/htslib-1.x/cram/zfio.h
pysam/htslib-1.x/htslib/bgzf.h
pysam/htslib-1.x/htslib/faidx.h
pysam/htslib-1.x/htslib/hfile.h
pysam/htslib-1.x/htslib/hts.h
pysam/htslib-1.x/htslib/hts_defs.h
pysam/htslib-1.x/htslib/kfunc.h
pysam/htslib-1.x/htslib/khash.h
pysam/htslib-1.x/htslib/khash_str2int.h
pysam/htslib-1.x/htslib/klist.h
pysam/htslib-1.x/htslib/knetfile.h
pysam/htslib-1.x/htslib/kseq.h
pysam/htslib-1.x/htslib/ksort.h
pysam/htslib-1.x/htslib/kstring.h
pysam/htslib-1.x/htslib/regidx.h
pysam/htslib-1.x/htslib/sam.h
pysam/htslib-1.x/htslib/synced_bcf_reader.h
pysam/htslib-1.x/htslib/tbx.h
pysam/htslib-1.x/htslib/vcf.h
pysam/htslib-1.x/htslib/vcf_sweep.h
pysam/htslib-1.x/htslib/vcfutils.h
pysam/pysam/COPYING_PYSAM
pysam/pysam/Pileup.py
pysam/pysam/TabProxies.c
pysam/pysam/__init__.py
pysam/pysam/csamtools.c
pysam/pysam/ctabix.c
pysam/pysam/cvcf.c
pysam/pysam/pysam_util.c
pysam/pysam/pysam_util.h
pysam/pysam/tabix_util.c
pysam/pysam/tabix_util.h
pysam/pysam/version.py
pysam/pysam/include/__init__.py
pysam/samtools/AUTHORS
pysam/samtools/COPYING
pysam/samtools/Makefile
pysam/samtools/NEWS
pysam/samtools/__init__.py
pysam/samtools/bam.c
pysam/samtools/bam.h
pysam/samtools/bam2bcf.c
pysam/samtools/bam2bcf.h
pysam/samtools/bam2bcf_indel.c
pysam/samtools/bam2depth.c
pysam/samtools/bam_aux.c
pysam/samtools/bam_cat.c
pysam/samtools/bam_color.c
pysam/samtools/bam_endian.h
pysam/samtools/bam_import.c
pysam/samtools/bam_index.c
pysam/samtools/bam_lpileup.c
pysam/samtools/bam_mate.c
pysam/samtools/bam_md.c
pysam/samtools/bam_pileup.c
pysam/samtools/bam_plcmd.c
pysam/samtools/bam_reheader.c
pysam/samtools/bam_rmdup.c
pysam/samtools/bam_rmdupse.c
pysam/samtools/bam_sort.c
pysam/samtools/bam_stat.c
pysam/samtools/bam_tview.c
pysam/samtools/bam_tview.h
pysam/samtools/bam_tview_curses.c
pysam/samtools/bam_tview_html.c
pysam/samtools/bamshuf.c
pysam/samtools/bamtk.c
pysam/samtools/bedcov.c
pysam/samtools/bedidx.c
pysam/samtools/bgzf.c
pysam/samtools/bgzf.h
pysam/samtools/bgzip.c
pysam/samtools/cut_target.c
pysam/samtools/errmod.c
pysam/samtools/errmod.h
pysam/samtools/faidx.c
pysam/samtools/faidx.h
pysam/samtools/kaln.c
pysam/samtools/kaln.h
pysam/samtools/khash.h
pysam/samtools/klist.h
pysam/samtools/knetfile.c
pysam/samtools/knetfile.h
pysam/samtools/kprobaln.c
pysam/samtools/kprobaln.h
pysam/samtools/kseq.h
pysam/samtools/ksort.h
pysam/samtools/kstring.c
pysam/samtools/kstring.h
pysam/samtools/padding.c
pysam/samtools/phase.c
pysam/samtools/pysam.h
pysam/samtools/razf.c
pysam/samtools/razf.h
pysam/samtools/razip.c
pysam/samtools/sam.c
pysam/samtools/sam.h
pysam/samtools/sam_header.c
pysam/samtools/sam_header.h
pysam/samtools/sam_view.c
pysam/samtools/sample.c
pysam/samtools/sample.h
pysam/samtools/samtools.1
pysam/samtools-1.x/AUTHORS
pysam/samtools-1.x/ChangeLog.old
pysam/samtools-1.x/INSTALL
pysam/samtools-1.x/LICENSE
pysam/samtools-1.x/Makefile
pysam/samtools-1.x/Makefile.mingw
pysam/samtools-1.x/NEWS
pysam/samtools-1.x/README
pysam/samtools-1.x/bam.c
pysam/samtools-1.x/bam.h
pysam/samtools-1.x/bam2bcf.c
pysam/samtools-1.x/bam2bcf.h
pysam/samtools-1.x/bam2bcf_indel.c
pysam/samtools-1.x/bam2depth.c
pysam/samtools-1.x/bam_aux.c
pysam/samtools-1.x/bam_cat.c
pysam/samtools-1.x/bam_color.c
pysam/samtools-1.x/bam_endian.h
pysam/samtools-1.x/bam_flags.c
pysam/samtools-1.x/bam_import.c
pysam/samtools-1.x/bam_index.c
pysam/samtools-1.x/bam_lpileup.c
pysam/samtools-1.x/bam_lpileup.h
pysam/samtools-1.x/bam_mate.c
pysam/samtools-1.x/bam_md.c
pysam/samtools-1.x/bam_plbuf.c
pysam/samtools-1.x/bam_plbuf.h
pysam/samtools-1.x/bam_plcmd.c
pysam/samtools-1.x/bam_reheader.c
pysam/samtools-1.x/bam_rmdup.c
pysam/samtools-1.x/bam_rmdupse.c
pysam/samtools-1.x/bam_sort.c
pysam/samtools-1.x/bam_split.c
pysam/samtools-1.x/bam_stat.c
pysam/samtools-1.x/bam_tview.c
pysam/samtools-1.x/bam_tview.h
pysam/samtools-1.x/bam_tview_curses.c
pysam/samtools-1.x/bam_tview_html.c
pysam/samtools-1.x/bamshuf.c
pysam/samtools-1.x/bamtk.c
pysam/samtools-1.x/bedcov.c
pysam/samtools-1.x/bedidx.c
pysam/samtools-1.x/cut_target.c
pysam/samtools-1.x/errmod.c
pysam/samtools-1.x/errmod.h
pysam/samtools-1.x/faidx.c
pysam/samtools-1.x/kprobaln.c
pysam/samtools-1.x/kprobaln.h
pysam/samtools-1.x/padding.c
pysam/samtools-1.x/phase.c
pysam/samtools-1.x/sam.c
pysam/samtools-1.x/sam.h
pysam/samtools-1.x/sam_header.c
pysam/samtools-1.x/sam_header.h
pysam/samtools-1.x/sam_view.c
pysam/samtools-1.x/sample.c
pysam/samtools-1.x/sample.h
pysam/samtools-1.x/samtools.1
pysam/samtools-1.x/samtools.h
pysam/samtools-1.x/stats.c
pysam/samtools-1.x/stats_isize.c
pysam/samtools-1.x/stats_isize.h
pysam/samtools/bcftools/Makefile
pysam/samtools/bcftools/__init__.py
pysam/samtools/bcftools/bcf.c
pysam/samtools/bcftools/bcf.h
pysam/samtools/bcftools/bcf2qcall.c
pysam/samtools/bcftools/bcfutils.c
pysam/samtools/bcftools/call1.c
pysam/samtools/bcftools/em.c
pysam/samtools/bcftools/fet.c
pysam/samtools/bcftools/index.c
pysam/samtools/bcftools/kfunc.c
pysam/samtools/bcftools/kmin.c
pysam/samtools/bcftools/kmin.h
pysam/samtools/bcftools/main.c
pysam/samtools/bcftools/mut.c
pysam/samtools/bcftools/prob1.c
pysam/samtools/bcftools/prob1.h
pysam/samtools/bcftools/vcf.c
scr/mimodd
snap/COPYING
snap/LICENSE
snap/Makefile
snap/snap.sln
snap/SNAPLib/Aligner.h
snap/SNAPLib/AlignerContext.cpp
snap/SNAPLib/AlignerContext.d
snap/SNAPLib/AlignerContext.h
snap/SNAPLib/AlignerOptions.cpp
snap/SNAPLib/AlignerOptions.d
snap/SNAPLib/AlignerOptions.h
snap/SNAPLib/AlignerStats.cpp
snap/SNAPLib/AlignerStats.d
snap/SNAPLib/AlignerStats.h
snap/SNAPLib/ApproximateCounter.cpp
snap/SNAPLib/ApproximateCounter.d
snap/SNAPLib/ApproximateCounter.h
snap/SNAPLib/BaseAligner.cpp
snap/SNAPLib/BaseAligner.d
snap/SNAPLib/BaseAligner.h
snap/SNAPLib/BiasTables.cpp
snap/SNAPLib/BiasTables.d
snap/SNAPLib/BigAlloc.cpp
snap/SNAPLib/BigAlloc.d
snap/SNAPLib/BigAlloc.h
snap/SNAPLib/BoundedStringDistance.h
snap/SNAPLib/BufferedAsync.cpp
snap/SNAPLib/BufferedAsync.d
snap/SNAPLib/BufferedAsync.h
snap/SNAPLib/Chrom.h
snap/SNAPLib/Cigar.cpp
snap/SNAPLib/Cigar.d
snap/SNAPLib/Cigar.h
snap/SNAPLib/Compat.cpp
snap/SNAPLib/Compat.d
snap/SNAPLib/Compat.h
snap/SNAPLib/FASTA.cpp
snap/SNAPLib/FASTA.d
snap/SNAPLib/FASTA.h
snap/SNAPLib/FASTQ.cpp
snap/SNAPLib/FASTQ.d
snap/SNAPLib/FASTQ.h
snap/SNAPLib/FixedSizeMap.h
snap/SNAPLib/FixedSizeSet.h
snap/SNAPLib/FixedSizeVector.h
snap/SNAPLib/Genome.cpp
snap/SNAPLib/Genome.d
snap/SNAPLib/Genome.h
snap/SNAPLib/GenomeIndex.cpp
snap/SNAPLib/GenomeIndex.d
snap/SNAPLib/GenomeIndex.h
snap/SNAPLib/GoodRandom.cpp
snap/SNAPLib/GoodRandom.d
snap/SNAPLib/GoodRandom.h
snap/SNAPLib/GtypeBank.cpp
snap/SNAPLib/GtypeBank.d
snap/SNAPLib/GtypeBank.h
snap/SNAPLib/HashTable.cpp
snap/SNAPLib/HashTable.d
snap/SNAPLib/HashTable.h
snap/SNAPLib/Histogram.cpp
snap/SNAPLib/Histogram.d
snap/SNAPLib/Histogram.h
snap/SNAPLib/HybridAligner.cpp
snap/SNAPLib/HybridAligner.d
snap/SNAPLib/HybridAligner.h
snap/SNAPLib/IntersectingAligner.cpp
snap/SNAPLib/IntersectingAligner.d
snap/SNAPLib/IntersectingAligner.h
snap/SNAPLib/LandauVishkin.cpp
snap/SNAPLib/LandauVishkin.d
snap/SNAPLib/LandauVishkin.h
snap/SNAPLib/Mutation.h
snap/SNAPLib/Mutator.cpp
snap/SNAPLib/Mutator.d
snap/SNAPLib/Mutator.h
snap/SNAPLib/OffsetMap.h
snap/SNAPLib/OldAligner.cpp
snap/SNAPLib/OldAligner.d
snap/SNAPLib/OldAligner.h
snap/SNAPLib/PairedAligner.cpp
snap/SNAPLib/PairedAligner.d
snap/SNAPLib/PairedAligner.h
snap/SNAPLib/PairedEndAligner.cpp
snap/SNAPLib/PairedEndAligner.d
snap/SNAPLib/PairedEndAligner.h
snap/SNAPLib/ParallelTask.h
snap/SNAPLib/Range.cpp
snap/SNAPLib/Range.d
snap/SNAPLib/Range.h
snap/SNAPLib/RangeSplitter.cpp
snap/SNAPLib/RangeSplitter.d
snap/SNAPLib/RangeSplitter.h
snap/SNAPLib/Read.h
snap/SNAPLib/ReadMe.txt
snap/SNAPLib/SAM.cpp
snap/SNAPLib/SAM.cpp.orig
snap/SNAPLib/SAM.cpp~
snap/SNAPLib/SAM.d
snap/SNAPLib/SAM.h
snap/SNAPLib/SNAPLib.vcxproj
snap/SNAPLib/SNAPLib.vcxproj.filters
snap/SNAPLib/Seed.cpp
snap/SNAPLib/Seed.d
snap/SNAPLib/Seed.h
snap/SNAPLib/SimplePairedEndAligner.cpp
snap/SNAPLib/SimplePairedEndAligner.d
snap/SNAPLib/SimplePairedEndAligner.h
snap/SNAPLib/SingleAligner.cpp
snap/SNAPLib/SingleAligner.d
snap/SNAPLib/SingleAligner.h
snap/SNAPLib/SmarterPairedEndAligner.cpp
snap/SNAPLib/SmarterPairedEndAligner.d
snap/SNAPLib/SmarterPairedEndAligner.h
snap/SNAPLib/Tables.cpp
snap/SNAPLib/Tables.d
snap/SNAPLib/Tables.h
snap/SNAPLib/Util.h
snap/SNAPLib/VCF.cpp
snap/SNAPLib/VCF.d
snap/SNAPLib/VCF.h
snap/SNAPLib/VariableSizeVector.h
snap/SNAPLib/WGsim.cpp
snap/SNAPLib/WGsim.d
snap/SNAPLib/WGsim.h
snap/SNAPLib/mt19937-64.cpp
snap/SNAPLib/mt19937-64.d
snap/SNAPLib/mt64.h
snap/SNAPLib/options.h
snap/SNAPLib/stdafx.cpp
snap/SNAPLib/stdafx.d
snap/SNAPLib/stdafx.h
snap/SNAPLib/targetver.h
snap/apps/snap/Main.cpp
snap/apps/snap/Main.d
snap/apps/snap/snap.vcxproj
snap/apps/snap/snap.vcxproj.filters
snap/apps/snap/stdafx.cpp
snap/apps/snap/stdafx.d
snap/apps/snap/stdafx.h
snap/apps/snap/targetver.h
snap/tests/BoundedStringDistanceTest.cpp
snap/tests/BoundedStringDistanceTest.d
snap/tests/LandauVishkinTest.cpp
snap/tests/LandauVishkinTest.d
snap/tests/OffsetMapTest.cpp
snap/tests/OffsetMapTest.d
snap/tests/TestLib.cpp
snap/tests/TestLib.d
snap/tests/TestLib.h
snap/tests/main.cpp
snap/tests/main.d