LICENSE
MANIFEST.in
README.md
setup.py
bsbolt/__init__.py
bsbolt/__main__.py
bsbolt.egg-info/PKG-INFO
bsbolt.egg-info/SOURCES.txt
bsbolt.egg-info/dependency_links.txt
bsbolt.egg-info/entry_points.txt
bsbolt.egg-info/not-zip-safe
bsbolt.egg-info/requires.txt
bsbolt.egg-info/top_level.txt
bsbolt/Align/AlignReads.py
bsbolt/Align/__init__.py
bsbolt/CallMethylation/CallValues.py
bsbolt/CallMethylation/CallVector.py
bsbolt/CallMethylation/ProcessMethylationContigs.py
bsbolt/CallMethylation/__init__.py
bsbolt/External/BWA/COPYING
bsbolt/External/BWA/Makefile
bsbolt/External/BWA/QSufSort.c
bsbolt/External/BWA/QSufSort.h
bsbolt/External/BWA/bntseq.c
bsbolt/External/BWA/bntseq.h
bsbolt/External/BWA/bs_helpers.cpp
bsbolt/External/BWA/bs_helpers.h
bsbolt/External/BWA/bs_sorter.cpp
bsbolt/External/BWA/bs_sorter.h
bsbolt/External/BWA/bs_sorter_wrapper.cpp
bsbolt/External/BWA/bs_sorter_wrapper.h
bsbolt/External/BWA/bwa.c
bsbolt/External/BWA/bwa.h
bsbolt/External/BWA/bwamem.c
bsbolt/External/BWA/bwamem.h
bsbolt/External/BWA/bwamem_extra.c
bsbolt/External/BWA/bwamem_pair.c
bsbolt/External/BWA/bwashm.c
bsbolt/External/BWA/bwt.c
bsbolt/External/BWA/bwt.h
bsbolt/External/BWA/bwt_gen.c
bsbolt/External/BWA/bwtindex.c
bsbolt/External/BWA/fastmap.c
bsbolt/External/BWA/fastmap.h
bsbolt/External/BWA/is.c
bsbolt/External/BWA/kbtree.h
bsbolt/External/BWA/khash.h
bsbolt/External/BWA/kopen.c
bsbolt/External/BWA/kseq.h
bsbolt/External/BWA/ksort.h
bsbolt/External/BWA/kstring.c
bsbolt/External/BWA/kstring.h
bsbolt/External/BWA/ksw.c
bsbolt/External/BWA/ksw.h
bsbolt/External/BWA/kthread.c
bsbolt/External/BWA/kvec.h
bsbolt/External/BWA/main.c
bsbolt/External/BWA/malloc_wrap.c
bsbolt/External/BWA/malloc_wrap.h
bsbolt/External/BWA/rle.c
bsbolt/External/BWA/rle.h
bsbolt/External/BWA/rope.c
bsbolt/External/BWA/rope.h
bsbolt/External/BWA/utils.c
bsbolt/External/BWA/utils.h
bsbolt/External/HTSLIB/INSTALL
bsbolt/External/HTSLIB/LICENSE
bsbolt/External/HTSLIB/Makefile
bsbolt/External/HTSLIB/bcf_sr_sort.c
bsbolt/External/HTSLIB/bcf_sr_sort.h
bsbolt/External/HTSLIB/bgzf.c
bsbolt/External/HTSLIB/bgzip.1
bsbolt/External/HTSLIB/bgzip.c
bsbolt/External/HTSLIB/config.mk.in
bsbolt/External/HTSLIB/configure.ac
bsbolt/External/HTSLIB/errmod.c
bsbolt/External/HTSLIB/faidx.5
bsbolt/External/HTSLIB/faidx.c
bsbolt/External/HTSLIB/header.c
bsbolt/External/HTSLIB/header.h
bsbolt/External/HTSLIB/hfile.c
bsbolt/External/HTSLIB/hfile_gcs.c
bsbolt/External/HTSLIB/hfile_internal.h
bsbolt/External/HTSLIB/hfile_libcurl.c
bsbolt/External/HTSLIB/hfile_net.c
bsbolt/External/HTSLIB/hfile_s3.c
bsbolt/External/HTSLIB/hfile_s3_write.c
bsbolt/External/HTSLIB/hts.c
bsbolt/External/HTSLIB/hts_internal.h
bsbolt/External/HTSLIB/hts_os.c
bsbolt/External/HTSLIB/htsfile.1
bsbolt/External/HTSLIB/htsfile.c
bsbolt/External/HTSLIB/htslib-s3-plugin.7
bsbolt/External/HTSLIB/htslib.mk
bsbolt/External/HTSLIB/htslib.pc.in
bsbolt/External/HTSLIB/htslib_vars.mk
bsbolt/External/HTSLIB/kfunc.c
bsbolt/External/HTSLIB/knetfile.c
bsbolt/External/HTSLIB/kstring.c
bsbolt/External/HTSLIB/md5.c
bsbolt/External/HTSLIB/multipart.c
bsbolt/External/HTSLIB/plugin.c
bsbolt/External/HTSLIB/probaln.c
bsbolt/External/HTSLIB/realn.c
bsbolt/External/HTSLIB/regidx.c
bsbolt/External/HTSLIB/region.c
bsbolt/External/HTSLIB/sam.5
bsbolt/External/HTSLIB/sam.c
bsbolt/External/HTSLIB/sam_internal.h
bsbolt/External/HTSLIB/stream_bam.c
bsbolt/External/HTSLIB/synced_bcf_reader.c
bsbolt/External/HTSLIB/tabix.1
bsbolt/External/HTSLIB/tabix.c
bsbolt/External/HTSLIB/tbx.c
bsbolt/External/HTSLIB/textutils.c
bsbolt/External/HTSLIB/textutils_internal.h
bsbolt/External/HTSLIB/thread_pool.c
bsbolt/External/HTSLIB/thread_pool_internal.h
bsbolt/External/HTSLIB/vcf.5
bsbolt/External/HTSLIB/vcf.c
bsbolt/External/HTSLIB/vcf_sweep.c
bsbolt/External/HTSLIB/vcfutils.c
bsbolt/External/HTSLIB/version.sh
bsbolt/External/HTSLIB/cram/cram.h
bsbolt/External/HTSLIB/cram/cram_codecs.c
bsbolt/External/HTSLIB/cram/cram_codecs.h
bsbolt/External/HTSLIB/cram/cram_decode.c
bsbolt/External/HTSLIB/cram/cram_decode.h
bsbolt/External/HTSLIB/cram/cram_encode.c
bsbolt/External/HTSLIB/cram/cram_encode.h
bsbolt/External/HTSLIB/cram/cram_external.c
bsbolt/External/HTSLIB/cram/cram_index.c
bsbolt/External/HTSLIB/cram/cram_index.h
bsbolt/External/HTSLIB/cram/cram_io.c
bsbolt/External/HTSLIB/cram/cram_io.h
bsbolt/External/HTSLIB/cram/cram_samtools.c
bsbolt/External/HTSLIB/cram/cram_samtools.h
bsbolt/External/HTSLIB/cram/cram_stats.c
bsbolt/External/HTSLIB/cram/cram_stats.h
bsbolt/External/HTSLIB/cram/cram_structs.h
bsbolt/External/HTSLIB/cram/mFILE.c
bsbolt/External/HTSLIB/cram/mFILE.h
bsbolt/External/HTSLIB/cram/misc.h
bsbolt/External/HTSLIB/cram/open_trace_file.c
bsbolt/External/HTSLIB/cram/open_trace_file.h
bsbolt/External/HTSLIB/cram/os.h
bsbolt/External/HTSLIB/cram/pooled_alloc.c
bsbolt/External/HTSLIB/cram/pooled_alloc.h
bsbolt/External/HTSLIB/cram/rANS_byte.h
bsbolt/External/HTSLIB/cram/rANS_static.c
bsbolt/External/HTSLIB/cram/rANS_static.h
bsbolt/External/HTSLIB/cram/string_alloc.c
bsbolt/External/HTSLIB/cram/string_alloc.h
bsbolt/External/HTSLIB/htslib/bgzf.h
bsbolt/External/HTSLIB/htslib/cram.h
bsbolt/External/HTSLIB/htslib/faidx.h
bsbolt/External/HTSLIB/htslib/hfile.h
bsbolt/External/HTSLIB/htslib/hts.h
bsbolt/External/HTSLIB/htslib/hts_defs.h
bsbolt/External/HTSLIB/htslib/hts_endian.h
bsbolt/External/HTSLIB/htslib/hts_log.h
bsbolt/External/HTSLIB/htslib/hts_os.h
bsbolt/External/HTSLIB/htslib/kbitset.h
bsbolt/External/HTSLIB/htslib/kfunc.h
bsbolt/External/HTSLIB/htslib/khash.h
bsbolt/External/HTSLIB/htslib/khash_str2int.h
bsbolt/External/HTSLIB/htslib/klist.h
bsbolt/External/HTSLIB/htslib/knetfile.h
bsbolt/External/HTSLIB/htslib/kroundup.h
bsbolt/External/HTSLIB/htslib/kseq.h
bsbolt/External/HTSLIB/htslib/ksort.h
bsbolt/External/HTSLIB/htslib/kstring.h
bsbolt/External/HTSLIB/htslib/regidx.h
bsbolt/External/HTSLIB/htslib/sam.h
bsbolt/External/HTSLIB/htslib/synced_bcf_reader.h
bsbolt/External/HTSLIB/htslib/tbx.h
bsbolt/External/HTSLIB/htslib/thread_pool.h
bsbolt/External/HTSLIB/htslib/vcf.h
bsbolt/External/HTSLIB/htslib/vcf_sweep.h
bsbolt/External/HTSLIB/htslib/vcfutils.h
bsbolt/External/HTSLIB/m4/hts_hide_dynamic_syms.m4
bsbolt/External/HTSLIB/m4/hts_prog_cc_warnings.m4
bsbolt/External/HTSLIB/m4/pkg.m4
bsbolt/External/HTSLIB/os/lzma_stub.h
bsbolt/External/HTSLIB/os/rand.c
bsbolt/External/HTSLIB/test/auxf.fa
bsbolt/External/HTSLIB/test/auxf.fa.fai
bsbolt/External/HTSLIB/test/bgziptest.txt
bsbolt/External/HTSLIB/test/bgziptest.txt.gz
bsbolt/External/HTSLIB/test/bgziptest.txt.gz.gzi
bsbolt/External/HTSLIB/test/c1.fa
bsbolt/External/HTSLIB/test/c1.fa.fai
bsbolt/External/HTSLIB/test/c2.fa
bsbolt/External/HTSLIB/test/c2.fa.fai
bsbolt/External/HTSLIB/test/ce.fa
bsbolt/External/HTSLIB/test/ce.fa.fai
bsbolt/External/HTSLIB/test/colons.bam
bsbolt/External/HTSLIB/test/colons.bam.bai
bsbolt/External/HTSLIB/test/compare_sam.pl
bsbolt/External/HTSLIB/test/cross_validate.sh
bsbolt/External/HTSLIB/test/emptyfile
bsbolt/External/HTSLIB/test/faidx.fa
bsbolt/External/HTSLIB/test/fastqs.fq
bsbolt/External/HTSLIB/test/fastqs_README.txt
bsbolt/External/HTSLIB/test/fieldarith.c
bsbolt/External/HTSLIB/test/fieldarith.sam
bsbolt/External/HTSLIB/test/formatcols.vcf
bsbolt/External/HTSLIB/test/formatmissing-out.vcf
bsbolt/External/HTSLIB/test/formatmissing.vcf
bsbolt/External/HTSLIB/test/header_syms.pl
bsbolt/External/HTSLIB/test/hfile.c
bsbolt/External/HTSLIB/test/hts_endian.c
bsbolt/External/HTSLIB/test/index.bam.bai
bsbolt/External/HTSLIB/test/index.bam.csi
bsbolt/External/HTSLIB/test/index.bcf.csi
bsbolt/External/HTSLIB/test/index.cram.crai
bsbolt/External/HTSLIB/test/index.sam
bsbolt/External/HTSLIB/test/index.sam.gz.bai
bsbolt/External/HTSLIB/test/index.sam.gz.csi
bsbolt/External/HTSLIB/test/index.vcf
bsbolt/External/HTSLIB/test/index.vcf.gz.csi
bsbolt/External/HTSLIB/test/index.vcf.gz.tbi
bsbolt/External/HTSLIB/test/md.fa
bsbolt/External/HTSLIB/test/md.fa.fai
bsbolt/External/HTSLIB/test/no_hdr_sq_1.bam
bsbolt/External/HTSLIB/test/no_hdr_sq_1.bam.csi
bsbolt/External/HTSLIB/test/no_hdr_sq_1.expected.sam
bsbolt/External/HTSLIB/test/noroundtrip-out.vcf
bsbolt/External/HTSLIB/test/noroundtrip.vcf
bsbolt/External/HTSLIB/test/pileup.c
bsbolt/External/HTSLIB/test/range.bam
bsbolt/External/HTSLIB/test/range.bam.bai
bsbolt/External/HTSLIB/test/range.cram
bsbolt/External/HTSLIB/test/range.cram.crai
bsbolt/External/HTSLIB/test/range.out
bsbolt/External/HTSLIB/test/realn01.fa
bsbolt/External/HTSLIB/test/realn01.fa.fai
bsbolt/External/HTSLIB/test/realn01.sam
bsbolt/External/HTSLIB/test/realn01_exp-a.sam
bsbolt/External/HTSLIB/test/realn01_exp-e.sam
bsbolt/External/HTSLIB/test/realn01_exp.sam
bsbolt/External/HTSLIB/test/realn02-r.sam
bsbolt/External/HTSLIB/test/realn02.fa
bsbolt/External/HTSLIB/test/realn02.fa.fai
bsbolt/External/HTSLIB/test/realn02.sam
bsbolt/External/HTSLIB/test/realn02_exp-a.sam
bsbolt/External/HTSLIB/test/realn02_exp-e.sam
bsbolt/External/HTSLIB/test/realn02_exp.sam
bsbolt/External/HTSLIB/test/sam.c
bsbolt/External/HTSLIB/test/simple_test_driver.sh
bsbolt/External/HTSLIB/test/tabix.out
bsbolt/External/HTSLIB/test/test-bcf-sr.c
bsbolt/External/HTSLIB/test/test-bcf-sr.pl
bsbolt/External/HTSLIB/test/test-bcf-translate.c
bsbolt/External/HTSLIB/test/test-bcf-translate.out
bsbolt/External/HTSLIB/test/test-logging.pl
bsbolt/External/HTSLIB/test/test-parse-reg.c
bsbolt/External/HTSLIB/test/test-regidx.c
bsbolt/External/HTSLIB/test/test-vcf-api.c
bsbolt/External/HTSLIB/test/test-vcf-api.out
bsbolt/External/HTSLIB/test/test-vcf-hdr-in.vcf
bsbolt/External/HTSLIB/test/test-vcf-hdr.out
bsbolt/External/HTSLIB/test/test-vcf-sweep.c
bsbolt/External/HTSLIB/test/test-vcf-sweep.out
bsbolt/External/HTSLIB/test/test.pl
bsbolt/External/HTSLIB/test/test_bgzf.c
bsbolt/External/HTSLIB/test/test_index.c
bsbolt/External/HTSLIB/test/test_kstring.c
bsbolt/External/HTSLIB/test/test_realn.c
bsbolt/External/HTSLIB/test/test_str2int.c
bsbolt/External/HTSLIB/test/test_view.c
bsbolt/External/HTSLIB/test/thrash_threads1.c
bsbolt/External/HTSLIB/test/thrash_threads2.c
bsbolt/External/HTSLIB/test/thrash_threads3.c
bsbolt/External/HTSLIB/test/thrash_threads4.c
bsbolt/External/HTSLIB/test/thrash_threads5.c
bsbolt/External/HTSLIB/test/thrash_threads6.c
bsbolt/External/HTSLIB/test/thrash_threads7.c
bsbolt/External/HTSLIB/test/thread_pool.md
bsbolt/External/HTSLIB/test/xx.fa
bsbolt/External/HTSLIB/test/xx.fa.fai
bsbolt/External/HTSLIB/test/fuzz/hts_open_fuzzer.c
bsbolt/External/HTSLIB/test/longrefs/index.expected1.vcf
bsbolt/External/HTSLIB/test/longrefs/index.expected2.vcf
bsbolt/External/HTSLIB/test/longrefs/index.vcf
bsbolt/External/HTSLIB/test/longrefs/longref.sam
bsbolt/External/HTSLIB/test/longrefs/longref_itr.expected.sam
bsbolt/External/HTSLIB/test/longrefs/longref_multi.expected.sam
bsbolt/External/HTSLIB/test/maintainer/check_copyright.pl
bsbolt/External/HTSLIB/test/maintainer/check_spaces.pl
bsbolt/External/HTSLIB/test/mpileup/mp_D.out
bsbolt/External/HTSLIB/test/mpileup/mp_D.sam
bsbolt/External/HTSLIB/test/mpileup/mp_DI.out
bsbolt/External/HTSLIB/test/mpileup/mp_DI.sam
bsbolt/External/HTSLIB/test/mpileup/mp_I.out
bsbolt/External/HTSLIB/test/mpileup/mp_I.sam
bsbolt/External/HTSLIB/test/mpileup/mp_ID.out
bsbolt/External/HTSLIB/test/mpileup/mp_ID.sam
bsbolt/External/HTSLIB/test/mpileup/mp_N.out
bsbolt/External/HTSLIB/test/mpileup/mp_N.sam
bsbolt/External/HTSLIB/test/mpileup/mp_N2.out
bsbolt/External/HTSLIB/test/mpileup/mp_N2.sam
bsbolt/External/HTSLIB/test/mpileup/mp_P.out
bsbolt/External/HTSLIB/test/mpileup/mp_P.sam
bsbolt/External/HTSLIB/test/mpileup/mpileup.tst
bsbolt/External/HTSLIB/test/mpileup/small.bam
bsbolt/External/HTSLIB/test/mpileup/small.out
bsbolt/External/HTSLIB/test/mpileup/test-pileup.sh
bsbolt/External/WGSIM/Makefile
bsbolt/External/WGSIM/src/kseq.h
bsbolt/External/WGSIM/src/wgsim.cpp
bsbolt/Impute/__init__.py
bsbolt/Impute/kNN_Impute.py
bsbolt/Impute/Imputation/EuclideanDistance.py
bsbolt/Impute/Imputation/GenomeImputation.py
bsbolt/Impute/Imputation/GenomeImputationWindows.py
bsbolt/Impute/Imputation/__init__.py
bsbolt/Impute/Impute_Utils/ImputationFunctions.py
bsbolt/Impute/Impute_Utils/__init__.py
bsbolt/Impute/Validation/ImputationAssessment.py
bsbolt/Impute/Validation/MaskValues.py
bsbolt/Impute/Validation/__init__.py
bsbolt/Index/IndexOutput.py
bsbolt/Index/RRBSCutSites.py
bsbolt/Index/RRBSIndex.py
bsbolt/Index/WholeGenomeIndex.py
bsbolt/Index/__init__.py
bsbolt/Matrix/MatrixAggregator.py
bsbolt/Matrix/SiteAggregator.py
bsbolt/Matrix/SiteCounter.py
bsbolt/Matrix/__init__.py
bsbolt/Simulate/SetCyotsineMethylation.py
bsbolt/Simulate/SimulateMethylatedReads.py
bsbolt/Simulate/SimulationOutput.py
bsbolt/Simulate/StreamSim.py
bsbolt/Simulate/__init__.py
bsbolt/Utils/AlignmentEvaluation.py
bsbolt/Utils/AlnIterator.py
bsbolt/Utils/CGmapIterator.py
bsbolt/Utils/FastaIterator.py
bsbolt/Utils/FastqIterator.py
bsbolt/Utils/Launcher.py
bsbolt/Utils/MatrixIterator.py
bsbolt/Utils/Parser.py
bsbolt/Utils/ParserHelpMessages.py
bsbolt/Utils/UtilityFunctions.py
bsbolt/Utils/__init__.py
bsbolt/Variant/BayesVariant.py
bsbolt/Variant/CallVariants.py
bsbolt/Variant/ProcessVariantRegions.py
bsbolt/Variant/VariantCall.py
bsbolt/Variant/__init__.py