LICENSE.md
MANIFEST.in
README.md
cy_build.py
setup.cfg
setup.py
htslib/Makefile
htslib/bcf_sr_sort.c
htslib/bcf_sr_sort.h
htslib/bgzf.c
htslib/bgzip.1
htslib/bgzip.c
htslib/config.h
htslib/config.h.in
htslib/config.mk
htslib/config.mk.in
htslib/config.status
htslib/config_vars.h
htslib/configure
htslib/configure.ac
htslib/errmod.c
htslib/faidx.5
htslib/faidx.c
htslib/header.c
htslib/header.h
htslib/hfile.c
htslib/hfile_gcs.c
htslib/hfile_internal.h
htslib/hfile_libcurl.c
htslib/hfile_s3.c
htslib/hfile_s3_write.c
htslib/hts.c
htslib/hts_expr.c
htslib/hts_internal.h
htslib/hts_os.c
htslib/htscodecs.mk
htslib/htscodecs.mk.in
htslib/htscodecs_bundled.mk
htslib/htscodecs_external.mk
htslib/htsfile.1
htslib/htsfile.c
htslib/htslib-s3-plugin.7
htslib/htslib.mk
htslib/htslib.pc.in
htslib/htslib_vars.mk
htslib/kfunc.c
htslib/kstring.c
htslib/md5.c
htslib/multipart.c
htslib/plugin.c
htslib/probaln.c
htslib/realn.c
htslib/regidx.c
htslib/region.c
htslib/sam.5
htslib/sam.c
htslib/sam_internal.h
htslib/synced_bcf_reader.c
htslib/tabix.1
htslib/tabix.c
htslib/tbx.c
htslib/textutils.c
htslib/textutils_internal.h
htslib/thread_pool.c
htslib/thread_pool_internal.h
htslib/vcf.5
htslib/vcf.c
htslib/vcf_sweep.c
htslib/vcfutils.c
htslib/version.h
htslib/version.sh
htslib/cram/cram.h
htslib/cram/cram_codecs.c
htslib/cram/cram_codecs.h
htslib/cram/cram_decode.c
htslib/cram/cram_decode.h
htslib/cram/cram_encode.c
htslib/cram/cram_encode.h
htslib/cram/cram_external.c
htslib/cram/cram_index.c
htslib/cram/cram_index.h
htslib/cram/cram_io.c
htslib/cram/cram_io.h
htslib/cram/cram_samtools.h
htslib/cram/cram_stats.c
htslib/cram/cram_stats.h
htslib/cram/cram_structs.h
htslib/cram/mFILE.c
htslib/cram/mFILE.h
htslib/cram/misc.h
htslib/cram/open_trace_file.c
htslib/cram/open_trace_file.h
htslib/cram/os.h
htslib/cram/pooled_alloc.c
htslib/cram/pooled_alloc.h
htslib/cram/string_alloc.c
htslib/cram/string_alloc.h
htslib/htscodecs/htscodecs/arith_dynamic.c
htslib/htscodecs/htscodecs/arith_dynamic.h
htslib/htscodecs/htscodecs/c_range_coder.h
htslib/htscodecs/htscodecs/c_simple_model.h
htslib/htscodecs/htscodecs/fqzcomp_qual.c
htslib/htscodecs/htscodecs/fqzcomp_qual.h
htslib/htscodecs/htscodecs/htscodecs.c
htslib/htscodecs/htscodecs/htscodecs.h
htslib/htscodecs/htscodecs/htscodecs_endian.h
htslib/htscodecs/htscodecs/pack.c
htslib/htscodecs/htscodecs/pack.h
htslib/htscodecs/htscodecs/pooled_alloc.h
htslib/htscodecs/htscodecs/rANS_byte.h
htslib/htscodecs/htscodecs/rANS_static.c
htslib/htscodecs/htscodecs/rANS_static.h
htslib/htscodecs/htscodecs/rANS_static4x16.h
htslib/htscodecs/htscodecs/rANS_static4x16pr.c
htslib/htscodecs/htscodecs/rANS_word.h
htslib/htscodecs/htscodecs/rle.c
htslib/htscodecs/htscodecs/rle.h
htslib/htscodecs/htscodecs/tokenise_name3.c
htslib/htscodecs/htscodecs/tokenise_name3.h
htslib/htscodecs/htscodecs/utils.h
htslib/htscodecs/htscodecs/varint.h
htslib/htscodecs/htscodecs/varint2.h
htslib/htscodecs/htscodecs/version.h
htslib/htscodecs/tests/arith_dynamic_fuzz.c
htslib/htscodecs/tests/arith_dynamic_test.c
htslib/htscodecs/tests/fqzcomp_qual_fuzz.c
htslib/htscodecs/tests/fqzcomp_qual_test.c
htslib/htscodecs/tests/rANS_static4x16pr_fuzz.c
htslib/htscodecs/tests/rANS_static4x16pr_test.c
htslib/htscodecs/tests/rANS_static_fuzz.c
htslib/htscodecs/tests/rANS_static_test.c
htslib/htscodecs/tests/tokenise_name3_fuzz.c
htslib/htscodecs/tests/tokenise_name3_test.c
htslib/htscodecs/tests/varint_test.c
htslib/htscodecs/tests/dat/arith/q4.1
htslib/htscodecs/tests/dat/arith/q40+dir.1
htslib/htscodecs/tests/dat/arith/q8.1
htslib/htscodecs/tests/dat/arith/qvar.1
htslib/htscodecs/tests/dat/fqzcomp/q4.1
htslib/htscodecs/tests/dat/fqzcomp/q40+dir.1
htslib/htscodecs/tests/dat/fqzcomp/q8.1
htslib/htscodecs/tests/dat/fqzcomp/qvar.1
htslib/htscodecs/tests/dat/r4x16/q4.1
htslib/htscodecs/tests/dat/r4x16/q40+dir.1
htslib/htscodecs/tests/dat/r4x16/q8.1
htslib/htscodecs/tests/dat/r4x16/qvar.1
htslib/htscodecs/tests/dat/r4x8/q4.1
htslib/htscodecs/tests/dat/r4x8/q40+dir.1
htslib/htscodecs/tests/dat/r4x8/q8.1
htslib/htscodecs/tests/dat/r4x8/qvar.1
htslib/htscodecs/tests/names/tok3/01.names.1
htslib/htscodecs/tests/names/tok3/01.names.5
htslib/htscodecs/tests/names/tok3/01.names.7
htslib/htscodecs/tests/names/tok3/02.names.1
htslib/htscodecs/tests/names/tok3/02.names.5
htslib/htscodecs/tests/names/tok3/02.names.7
htslib/htscodecs/tests/names/tok3/03.names.1
htslib/htscodecs/tests/names/tok3/03.names.5
htslib/htscodecs/tests/names/tok3/03.names.7
htslib/htscodecs/tests/names/tok3/05.names.1
htslib/htscodecs/tests/names/tok3/05.names.5
htslib/htscodecs/tests/names/tok3/05.names.7
htslib/htscodecs/tests/names/tok3/08.names.1
htslib/htscodecs/tests/names/tok3/08.names.5
htslib/htscodecs/tests/names/tok3/08.names.7
htslib/htscodecs/tests/names/tok3/09.names.1
htslib/htscodecs/tests/names/tok3/09.names.5
htslib/htscodecs/tests/names/tok3/09.names.7
htslib/htscodecs/tests/names/tok3/10.names.1
htslib/htscodecs/tests/names/tok3/10.names.5
htslib/htscodecs/tests/names/tok3/10.names.7
htslib/htscodecs/tests/names/tok3/20.names.1
htslib/htscodecs/tests/names/tok3/20.names.5
htslib/htscodecs/tests/names/tok3/20.names.7
htslib/htscodecs/tests/names/tok3/nv.names.1
htslib/htscodecs/tests/names/tok3/nv.names.5
htslib/htscodecs/tests/names/tok3/nv.names.7
htslib/htscodecs/tests/names/tok3/nv2.names.1
htslib/htscodecs/tests/names/tok3/nv2.names.5
htslib/htscodecs/tests/names/tok3/nv2.names.7
htslib/htscodecs/tests/names/tok3/rr.names.1
htslib/htscodecs/tests/names/tok3/rr.names.5
htslib/htscodecs/tests/names/tok3/rr.names.7
htslib/htslib/bgzf.h
htslib/htslib/cram.h
htslib/htslib/faidx.h
htslib/htslib/hfile.h
htslib/htslib/hts.h
htslib/htslib/hts_defs.h
htslib/htslib/hts_endian.h
htslib/htslib/hts_expr.h
htslib/htslib/hts_log.h
htslib/htslib/hts_os.h
htslib/htslib/kbitset.h
htslib/htslib/kfunc.h
htslib/htslib/khash.h
htslib/htslib/khash_str2int.h
htslib/htslib/klist.h
htslib/htslib/knetfile.h
htslib/htslib/kroundup.h
htslib/htslib/kseq.h
htslib/htslib/ksort.h
htslib/htslib/kstring.h
htslib/htslib/regidx.h
htslib/htslib/sam.h
htslib/htslib/synced_bcf_reader.h
htslib/htslib/tbx.h
htslib/htslib/thread_pool.h
htslib/htslib/vcf.h
htslib/htslib/vcf_sweep.h
htslib/htslib/vcfutils.h
htslib/m4/hts_hide_dynamic_syms.m4
htslib/m4/hts_prog_cc_warnings.m4
htslib/m4/pkg.m4
htslib/os/lzma_stub.h
htslib/os/rand.c
htslib/test/cross_validate.sh
htslib/test/fieldarith.c
htslib/test/hfile.c
htslib/test/hts_endian.c
htslib/test/pileup.c
htslib/test/plugins-dlhts.c
htslib/test/sam.c
htslib/test/simple_test_driver.sh
htslib/test/test-bcf-sr.c
htslib/test/test-bcf-translate.c
htslib/test/test-parse-reg.c
htslib/test/test-regidx.c
htslib/test/test-vcf-api.c
htslib/test/test-vcf-sweep.c
htslib/test/test_bgzf.c
htslib/test/test_expr.c
htslib/test/test_index.c
htslib/test/test_introspection.c
htslib/test/test_kfunc.c
htslib/test/test_kstring.c
htslib/test/test_realn.c
htslib/test/test_str2int.c
htslib/test/test_view.c
htslib/test/thrash_threads1.c
htslib/test/thrash_threads2.c
htslib/test/thrash_threads3.c
htslib/test/thrash_threads4.c
htslib/test/thrash_threads5.c
htslib/test/thrash_threads6.c
htslib/test/thrash_threads7.c
htslib/test/with-shlib.sh
htslib/test/fuzz/hts_open_fuzzer.c
htslib/test/mpileup/test-pileup.sh
htslib/test/sam_filter/filter.sh
htslib/test/tabix/test-tabix.sh
ngsfragments/__init__.py
ngsfragments/config.py
ngsfragments/fragments.py
ngsfragments/utilities.py
ngsfragments.egg-info/PKG-INFO
ngsfragments.egg-info/SOURCES.txt
ngsfragments.egg-info/dependency_links.txt
ngsfragments.egg-info/not-zip-safe
ngsfragments.egg-info/requires.txt
ngsfragments.egg-info/top_level.txt
ngsfragments/data/__init__.py
ngsfragments/data/genome_query.py
ngsfragments/data/hg19_CTCF.bed.gz
ngsfragments/data/hg19_DNase.bed.gz
ngsfragments/data/hg19_QDNAseq_blacklisted.bed.gz
ngsfragments/data/hg19_QDNAseq_blacklisted_v0.bed.gz
ngsfragments/data/hg19_TFBS.bed.gz
ngsfragments/data/hg19_TSS.bed.gz
ngsfragments/data/hg19_centro.txt
ngsfragments/data/hg19_chrom_sizes.txt
ngsfragments/data/hg19_detail_genes.txt
ngsfragments/data/hg19_ucsc_bin100000.h5
ngsfragments/data/hg19_ucsc_bin1000000.h5
ngsfragments/data/import_data.py
ngsfragments/peak_calling/CallPeaks.c
ngsfragments/peak_calling/CallPeaks.pxd
ngsfragments/peak_calling/CallPeaks.pyx
ngsfragments/peak_calling/RunningMean.c
ngsfragments/peak_calling/RunningMean.pxd
ngsfragments/peak_calling/RunningMean.pyx
ngsfragments/peak_calling/RunningMedian.c
ngsfragments/peak_calling/RunningMedian.pxd
ngsfragments/peak_calling/RunningMedian.pyx
ngsfragments/peak_calling/__init__.py
ngsfragments/peak_calling/running_mean.c
ngsfragments/peak_calling/running_mean.h
ngsfragments/peak_calling/sklist_pd.c
ngsfragments/peak_calling/sklist_pd.h
ngsfragments/plot/__init__.py
ngsfragments/plot/plot_bokeh.py
ngsfragments/plot/plot_plt.py
ngsfragments/read_sam/ReadSam.c
ngsfragments/read_sam/ReadSam.pxd
ngsfragments/read_sam/ReadSam.pyx
ngsfragments/read_sam/__init__.py
ngsfragments/read_sam/read_intervals.c
ngsfragments/read_sam/read_intervals.h
ngsfragments/segment/__init__.py
ngsfragments/segment/cnv.py
ngsfragments/segment/cnv_utilities.py
ngsfragments/segment/correction.py
ngsfragments/segment/create_bin_metrics.py
ngsfragments/segment/smooth_cnv/smoothCNV.c
ngsfragments/segment/smooth_cnv/smoothCNV.h
ngsfragments/segment/smooth_cnv/smooth_cnv.c
ngsfragments/segment/smooth_cnv/smooth_cnv.pxd
ngsfragments/segment/smooth_cnv/smooth_cnv.pyx