MANIFEST.in
distribute_setup.py
setup.py
doc/CONTACTS
doc/COPYING
doc/INSTALL
doc/Manual
doc/THANKS
lib/psyco_full.py
lib/RSeQC.egg-info/PKG-INFO
lib/RSeQC.egg-info/SOURCES.txt
lib/RSeQC.egg-info/dependency_links.txt
lib/RSeQC.egg-info/not-zip-safe
lib/RSeQC.egg-info/top_level.txt
lib/bx/__init__.py
lib/bx/_seqmapping.c
lib/bx/_seqmapping.pyx
lib/bx/binned_array.py
lib/bx/binned_array_tests.py
lib/bx/bitset.c
lib/bx/bitset.pyx
lib/bx/bitset_builders.py
lib/bx/bitset_tests.py
lib/bx/bitset_utils.py
lib/bx/filter.py
lib/bx/gene_reader.py
lib/bx/interval_index_file.py
lib/bx/interval_index_file_tests.py
lib/bx/seqmapping.py
lib/bx/seqmapping_tests.py
lib/bx/wiggle.py
lib/bx/wiggle_tests.py
lib/bx/align/__init__.py
lib/bx/align/_core.c
lib/bx/align/_core.pyx
lib/bx/align/_epo.c
lib/bx/align/_epo.pyx
lib/bx/align/axt.py
lib/bx/align/core.py
lib/bx/align/epo.py
lib/bx/align/epo_tests.py
lib/bx/align/lav.py
lib/bx/align/lav_tests.py
lib/bx/align/maf.py
lib/bx/align/maf_tests.py
lib/bx/align/score.py
lib/bx/align/score_tests.py
lib/bx/align/sitemask/__init__.py
lib/bx/align/sitemask/_cpg.c
lib/bx/align/sitemask/_cpg.pyx
lib/bx/align/sitemask/core.py
lib/bx/align/sitemask/cpg.py
lib/bx/align/sitemask/find_cpg.c
lib/bx/align/sitemask/find_cpg.h
lib/bx/align/sitemask/quality.py
lib/bx/align/sitemask/sitemask_tests.py
lib/bx/align/tools/__init__.py
lib/bx/align/tools/chop.py
lib/bx/align/tools/fuse.py
lib/bx/align/tools/thread.py
lib/bx/align/tools/tile.py
lib/bx/arrays/__init__.py
lib/bx/arrays/array_tree.c
lib/bx/arrays/array_tree.pyx
lib/bx/arrays/array_tree_tests.py
lib/bx/arrays/bed.c
lib/bx/arrays/bed.pyx
lib/bx/arrays/wiggle.c
lib/bx/arrays/wiggle.pyx
lib/bx/bbi/__init__.py
lib/bx/bbi/bbi_file.c
lib/bx/bbi/bbi_file.pyx
lib/bx/bbi/bigbed_file.c
lib/bx/bbi/bigbed_file.pyx
lib/bx/bbi/bigwig_file.c
lib/bx/bbi/bigwig_file.pyx
lib/bx/bbi/bigwig_tests.py
lib/bx/bbi/bpt_file.c
lib/bx/bbi/bpt_file.pyx
lib/bx/bbi/cirtree_file.c
lib/bx/bbi/cirtree_file.pyx
lib/bx/cookbook/__init__.py
lib/bx/cookbook/argparse.py
lib/bx/cookbook/attribute.py
lib/bx/cookbook/doc_optparse.py
lib/bx/cookbook/progress_bar.py
lib/bx/intervals/__init__.py
lib/bx/intervals/cluster.c
lib/bx/intervals/cluster.pyx
lib/bx/intervals/cluster_tests.py
lib/bx/intervals/intersection.c
lib/bx/intervals/intersection.pyx
lib/bx/intervals/intersection_tests.py
lib/bx/intervals/io.py
lib/bx/intervals/random_intervals.py
lib/bx/intervals/operations/__init__.py
lib/bx/intervals/operations/base_coverage.py
lib/bx/intervals/operations/complement.py
lib/bx/intervals/operations/concat.py
lib/bx/intervals/operations/coverage.py
lib/bx/intervals/operations/find_clusters.py
lib/bx/intervals/operations/intersect.py
lib/bx/intervals/operations/join.py
lib/bx/intervals/operations/merge.py
lib/bx/intervals/operations/quicksect.py
lib/bx/intervals/operations/subtract.py
lib/bx/intseq/__init__.py
lib/bx/intseq/ngramcount.c
lib/bx/intseq/ngramcount.pyx
lib/bx/misc/__init__.py
lib/bx/misc/_seekbzip2.c
lib/bx/misc/_seekbzip2.pyx
lib/bx/misc/bgzf.c
lib/bx/misc/bgzf.pyx
lib/bx/misc/bgzf_tests.py
lib/bx/misc/binary_file.py
lib/bx/misc/cdb.py
lib/bx/misc/cdb_tests.py
lib/bx/misc/filecache.py
lib/bx/misc/filecache_tests.py
lib/bx/misc/readlengths.py
lib/bx/misc/seekbzip2.py
lib/bx/misc/seekbzip2_tests.py
lib/bx/misc/seeklzop.py
lib/bx/misc/seeklzop_tests.py
lib/bx/motif/__init__.py
lib/bx/motif/_pwm.c
lib/bx/motif/_pwm.pyx
lib/bx/motif/pwm.py
lib/bx/motif/pwm_tests.py
lib/bx/motif/io/__init__.py
lib/bx/motif/io/transfac.py
lib/bx/motif/io/transfac_tests.py
lib/bx/motif/logo/__init__.py
lib/bx/motif/logo/template.ps
lib/bx/phylo/__init__.py
lib/bx/phylo/newick.py
lib/bx/phylo/newick_tests.py
lib/bx/phylo/phast.py
lib/bx/phylo/phast_tests.py
lib/bx/pwm/__init__.py
lib/bx/pwm/_position_weight_matrix.c
lib/bx/pwm/_position_weight_matrix.pyx
lib/bx/pwm/bed_score_aligned_pwm.py
lib/bx/pwm/bed_score_aligned_string.py
lib/bx/pwm/maf_select_motifs.py
lib/bx/pwm/position_weight_matrix.py
lib/bx/pwm/pwm_score_maf.py
lib/bx/pwm/pwm_score_motifs.py
lib/bx/pwm/pwm_score_positions.py
lib/bx/pwm/pwm_tests.py
lib/bx/seq/__init__.py
lib/bx/seq/_nib.c
lib/bx/seq/_nib.pyx
lib/bx/seq/_twobit.c
lib/bx/seq/_twobit.pyx
lib/bx/seq/core.py
lib/bx/seq/fasta.py
lib/bx/seq/fasta_tests.py
lib/bx/seq/nib.py
lib/bx/seq/nib_tests.py
lib/bx/seq/qdna.py
lib/bx/seq/qdna_tests.py
lib/bx/seq/seq.py
lib/bx/seq/seq_tests.py
lib/bx/seq/twobit.py
lib/bx/seq/twobit_tests.py
lib/bx/tabular/__init__.py
lib/bx/tabular/io.py
lib/bx_extras/__init__.py
lib/bx_extras/fpconst.py
lib/bx_extras/lrucache.py
lib/bx_extras/pstat.py
lib/bx_extras/pyparsing.py
lib/bx_extras/stats.py
lib/pysam/Pileup.py
lib/pysam/TabProxies.c
lib/pysam/TabProxies.pxd
lib/pysam/TabProxies.pyx
lib/pysam/__init__.py
lib/pysam/csamtools.c
lib/pysam/csamtools.pxd
lib/pysam/csamtools.pyx
lib/pysam/ctabix.c
lib/pysam/ctabix.pxd
lib/pysam/ctabix.pyx
lib/pysam/cvcf.c
lib/pysam/cvcf.pxd
lib/pysam/cvcf.pyx
lib/pysam/namedtuple.py
lib/pysam/pysam_util.c
lib/pysam/pysam_util.h
lib/pysam/tabix_util.c
lib/pysam/version.py
lib/qcmodule/BED.py
lib/qcmodule/FrameKmer.py
lib/qcmodule/PSL.py
lib/qcmodule/SAM.py
lib/qcmodule/__init__.py
lib/qcmodule/annoGene.py
lib/qcmodule/bam_cigar.py
lib/qcmodule/changePoint.py
lib/qcmodule/cigar.py
lib/qcmodule/dotProduct.py
lib/qcmodule/fasta.py
lib/qcmodule/fastq.py
lib/qcmodule/fickett.py
lib/qcmodule/mystat.py
lib/qcmodule/orf.py
lib/qcmodule/poisson.py
lib/qcmodule/quantile.py
lib/qcmodule/twoList.py
lib/qcmodule/wiggle.py
lib/samtools/bam.c.pysam.c
lib/samtools/bam.h
lib/samtools/bam2bcf.c.pysam.c
lib/samtools/bam2bcf.h
lib/samtools/bam2bcf_indel.c.pysam.c
lib/samtools/bam2depth.c.pysam.c
lib/samtools/bam_aux.c.pysam.c
lib/samtools/bam_cat.c.pysam.c
lib/samtools/bam_color.c.pysam.c
lib/samtools/bam_endian.h
lib/samtools/bam_import.c.pysam.c
lib/samtools/bam_index.c.pysam.c
lib/samtools/bam_lpileup.c.pysam.c
lib/samtools/bam_mate.c.pysam.c
lib/samtools/bam_md.c.pysam.c
lib/samtools/bam_pileup.c.pysam.c
lib/samtools/bam_plcmd.c.pysam.c
lib/samtools/bam_reheader.c.pysam.c
lib/samtools/bam_rmdup.c.pysam.c
lib/samtools/bam_rmdupse.c.pysam.c
lib/samtools/bam_sort.c.pysam.c
lib/samtools/bam_stat.c.pysam.c
lib/samtools/bam_tview.c.pysam.c
lib/samtools/bedidx.c.pysam.c
lib/samtools/bgzf.c.pysam.c
lib/samtools/bgzf.h
lib/samtools/cut_target.c.pysam.c
lib/samtools/errmod.c.pysam.c
lib/samtools/errmod.h
lib/samtools/faidx.c.pysam.c
lib/samtools/faidx.h
lib/samtools/kaln.c.pysam.c
lib/samtools/kaln.h
lib/samtools/khash.h
lib/samtools/klist.h
lib/samtools/knetfile.c.pysam.c
lib/samtools/knetfile.h
lib/samtools/kprobaln.c.pysam.c
lib/samtools/kprobaln.h
lib/samtools/kseq.h
lib/samtools/ksort.h
lib/samtools/kstring.c.pysam.c
lib/samtools/kstring.h
lib/samtools/phase.c.pysam.c
lib/samtools/pysam.h
lib/samtools/razf.c.pysam.c
lib/samtools/razf.h
lib/samtools/sam.c.pysam.c
lib/samtools/sam.h
lib/samtools/sam_header.c.pysam.c
lib/samtools/sam_header.h
lib/samtools/sam_view.c.pysam.c
lib/samtools/sample.c.pysam.c
lib/samtools/sample.h
lib/samtools/bcftools/bcf.c.pysam.c
lib/samtools/bcftools/bcf.h
lib/samtools/bcftools/bcf2qcall.c.pysam.c
lib/samtools/bcftools/bcfutils.c.pysam.c
lib/samtools/bcftools/call1.c.pysam.c
lib/samtools/bcftools/em.c.pysam.c
lib/samtools/bcftools/fet.c.pysam.c
lib/samtools/bcftools/index.c.pysam.c
lib/samtools/bcftools/kfunc.c.pysam.c
lib/samtools/bcftools/kmin.c.pysam.c
lib/samtools/bcftools/kmin.h
lib/samtools/bcftools/mut.c.pysam.c
lib/samtools/bcftools/prob1.c.pysam.c
lib/samtools/bcftools/prob1.h
lib/samtools/bcftools/vcf.c.pysam.c
lib/samtools/misc/md5.c.pysam.c
lib/samtools/misc/md5.h
lib/samtools/misc/seqtk.c.pysam.c
lib/samtools/win32/xcurses.h
lib/samtools/win32/zconf.h
lib/samtools/win32/zlib.h
lib/tabix/bam_endian.h
lib/tabix/bedidx.c.pysam.c
lib/tabix/bgzf.c.pysam.c
lib/tabix/bgzf.h
lib/tabix/bgzip.c.pysam.c
lib/tabix/index.c.pysam.c
lib/tabix/khash.h
lib/tabix/knetfile.c.pysam.c
lib/tabix/knetfile.h
lib/tabix/kseq.h
lib/tabix/ksort.h
lib/tabix/kstring.c.pysam.c
lib/tabix/kstring.h
lib/tabix/pysam.h
lib/tabix/tabix.h
lib/tests/00README.txt
lib/tests/Makefile
lib/tests/ex1.fa
lib/tests/ex1.sam.gz
lib/tests/ex10.sam
lib/tests/ex3.sam
lib/tests/ex4.sam
lib/tests/ex5.sam
lib/tests/ex6.sam
lib/tests/ex7.sam
lib/tests/ex8.sam
lib/tests/ex9_fail.bam
lib/tests/ex9_nofail.bam
lib/tests/example.gtf.gz
lib/tests/example.gtf.gz.tbi
lib/tests/example.py
lib/tests/pysam_test.py
lib/tests/segfault_tests.py
lib/tests/tabix_test.py
scripts/RPKM_count.py
scripts/RPKM_saturation.py
scripts/bam2wig.py
scripts/bam_stat.py
scripts/clipping_profile.py
scripts/divide_bam.py
scripts/geneBody_coverage.py
scripts/geneBody_coverage2.py
scripts/gtf2bed.py
scripts/infer_experiment.py
scripts/inner_distance.py
scripts/junction_annotation.py
scripts/junction_saturation.py
scripts/normalize_bigwig.py
scripts/overlay_bigwig.py
scripts/read_GC.py
scripts/read_NVC.py
scripts/read_distribution.py
scripts/read_duplication.py
scripts/read_hexamer.py
scripts/read_quality.py
scripts/split_bam.py
src/binBits.c
src/binBits.h
src/cluster.c
src/cluster.h
src/pwm_utils.c
src/pwm_utils.h
src/bunzip/micro-bunzip.c
src/bunzip/micro-bunzip.h
src/kent/bits.c
src/kent/bits.h
src/kent/common.c
src/kent/common.h
src/samtools/bgzf.c
src/samtools/bgzf.h
src/samtools/khash.h