LICENSE.md
README.md
setup.cfg
setup.py
data/genome_query.py
data/hg19_CTCF.bed.gz
data/hg19_DNase.bed.gz
data/hg19_QDNAseq_blacklisted.bed.gz
data/hg19_QDNAseq_blacklisted_v0.bed.gz
data/hg19_TFBS.bed.gz
data/hg19_TSS.bed.gz
data/hg19_centro.txt
data/hg19_chrom_sizes.txt
data/hg19_detail_genes.txt
data/hg19_ucsc_bin100000.h5
data/hg19_ucsc_bin1000000.h5
htslib/bcf_sr_sort.c
htslib/bcf_sr_sort.h
htslib/bgzf.c
htslib/config.h
htslib/config_vars.h
htslib/errmod.c
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/kfunc.c
htslib/kstring.c
htslib/md5.c
htslib/multipart.c
htslib/probaln.c
htslib/realn.c
htslib/regidx.c
htslib/region.c
htslib/sam.c
htslib/sam_internal.h
htslib/synced_bcf_reader.c
htslib/tbx.c
htslib/textutils.c
htslib/textutils_internal.h
htslib/thread_pool.c
htslib/thread_pool_internal.h
htslib/vcf.c
htslib/vcf_sweep.c
htslib/vcfutils.c
htslib/version.h
htslib/cram/cram_codecs.c
htslib/cram/cram_decode.c
htslib/cram/cram_encode.c
htslib/cram/cram_external.c
htslib/cram/cram_index.c
htslib/cram/cram_io.c
htslib/cram/cram_stats.c
htslib/cram/mFILE.c
htslib/cram/open_trace_file.c
htslib/cram/pooled_alloc.c
htslib/cram/string_alloc.c
htslib/htscodecs/htscodecs/arith_dynamic.c
htslib/htscodecs/htscodecs/fqzcomp_qual.c
htslib/htscodecs/htscodecs/htscodecs.c
htslib/htscodecs/htscodecs/pack.c
htslib/htscodecs/htscodecs/rANS_static.c
htslib/htscodecs/htscodecs/rANS_static4x16pr.c
htslib/htscodecs/htscodecs/rle.c
htslib/htscodecs/htscodecs/tokenise_name3.c
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
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/peak_calling/CallPeaks.pxd
ngsfragments/peak_calling/CallPeaks.pyx
ngsfragments/peak_calling/RunningMean.pxd
ngsfragments/peak_calling/RunningMean.pyx
ngsfragments/peak_calling/RunningMedian.pxd
ngsfragments/peak_calling/RunningMedian.pyx
ngsfragments/peak_calling/__init__.py
ngsfragments/peak_calling/running_mean.h
ngsfragments/peak_calling/sklist_pd.h
ngsfragments/plot/__init__.py
ngsfragments/plot/plot_bokeh.py
ngsfragments/plot/plot_plt.py
ngsfragments/read_sam/ReadSam.pxd
ngsfragments/read_sam/ReadSam.pyx
ngsfragments/read_sam/__init__.py
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/smooth_cnv.pyx