LICENSE
MANIFEST.in
README.md
setup.py
/Users/anzawa/github/PyMaSC/PyMaSC/bacore/bitarray.c
/Users/anzawa/github/PyMaSC/PyMaSC/bacore/mscc.c
/Users/anzawa/github/PyMaSC/PyMaSC/core/mappability.c
/Users/anzawa/github/PyMaSC/PyMaSC/core/mscc.c
/Users/anzawa/github/PyMaSC/PyMaSC/core/ncc.c
/Users/anzawa/github/PyMaSC/PyMaSC/core/readlen.c
/Users/anzawa/github/PyMaSC/PyMaSC/reader/bigwig.c
/Users/anzawa/github/PyMaSC/PyMaSC/reader/bx/bbi_file.c
/Users/anzawa/github/PyMaSC/PyMaSC/reader/bx/bigwig_file.c
/Users/anzawa/github/PyMaSC/PyMaSC/reader/bx/bpt_file.c
/Users/anzawa/github/PyMaSC/PyMaSC/utils/bx/binary_file.c
PyMaSC/__init__.py
PyMaSC/calcmappablelen.py
PyMaSC/plot.py
PyMaSC/pymasc.py
PyMaSC.egg-info/PKG-INFO
PyMaSC.egg-info/SOURCES.txt
PyMaSC.egg-info/dependency_links.txt
PyMaSC.egg-info/entry_points.txt
PyMaSC.egg-info/requires.txt
PyMaSC.egg-info/top_level.txt
PyMaSC/bacore/__init__.py
PyMaSC/bacore/bitarray.pxd
PyMaSC/bacore/bitarray.pyx
PyMaSC/bacore/bitarray_2.c
PyMaSC/bacore/bitarray_3.c
PyMaSC/bacore/mscc.pyx
PyMaSC/bacore/mscc_2.c
PyMaSC/bacore/mscc_3.c
PyMaSC/core/__init__.py
PyMaSC/core/mappability.pyx
PyMaSC/core/mappability_2.c
PyMaSC/core/mappability_3.c
PyMaSC/core/mscc.pyx
PyMaSC/core/mscc_2.c
PyMaSC/core/mscc_3.c
PyMaSC/core/ncc.pxd
PyMaSC/core/ncc.pyx
PyMaSC/core/ncc_2.c
PyMaSC/core/ncc_3.c
PyMaSC/core/readlen.pyx
PyMaSC/core/readlen_2.c
PyMaSC/core/readlen_3.c
PyMaSC/core/utils.pxd
PyMaSC/handler/__init__.py
PyMaSC/handler/bamasc.py
PyMaSC/handler/mappability.py
PyMaSC/handler/masc.py
PyMaSC/handler/masc_noindex_worker.py
PyMaSC/handler/masc_worker.py
PyMaSC/handler/result.py
PyMaSC/output/__init__.py
PyMaSC/output/figure.py
PyMaSC/output/stats.py
PyMaSC/reader/__init__.py
PyMaSC/reader/bigwig.pxd
PyMaSC/reader/bigwig.pyx
PyMaSC/reader/bigwig_2.c
PyMaSC/reader/bigwig_3.c
PyMaSC/reader/bx/__init__.py
PyMaSC/reader/bx/bbi_file.pxd
PyMaSC/reader/bx/bbi_file.pyx
PyMaSC/reader/bx/bbi_file_2.c
PyMaSC/reader/bx/bbi_file_3.c
PyMaSC/reader/bx/bigwig_file.pxd
PyMaSC/reader/bx/bigwig_file.pyx
PyMaSC/reader/bx/bigwig_file_2.c
PyMaSC/reader/bx/bigwig_file_3.c
PyMaSC/reader/bx/bpt_file.pxd
PyMaSC/reader/bx/bpt_file.pyx
PyMaSC/reader/bx/bpt_file_2.c
PyMaSC/reader/bx/bpt_file_3.c
PyMaSC/utils/__init__.py
PyMaSC/utils/calc.py
PyMaSC/utils/compatible.py
PyMaSC/utils/logfmt.py
PyMaSC/utils/output.py
PyMaSC/utils/parsearg.py
PyMaSC/utils/progress.py
PyMaSC/utils/bx/__init__.py
PyMaSC/utils/bx/binary_file.pxd
PyMaSC/utils/bx/binary_file.pyx
PyMaSC/utils/bx/binary_file_2.c
PyMaSC/utils/bx/binary_file_3.c
external/bitcnt.h
external/BitArray/AUTHORS
external/BitArray/LICENSE
external/BitArray/Makefile
external/BitArray/README.md
external/BitArray/bit_array.c
external/BitArray/bit_array.h
external/BitArray/bit_macros.h
external/bx-python/lib/bx/__init__.py
external/bx-python/lib/bx/_seqmapping.c
external/bx-python/lib/bx/_seqmapping.pyx
external/bx-python/lib/bx/binned_array.py
external/bx-python/lib/bx/binned_array_tests.py
external/bx-python/lib/bx/bitset.c
external/bx-python/lib/bx/bitset.pyx
external/bx-python/lib/bx/bitset_builders.py
external/bx-python/lib/bx/bitset_tests.py
external/bx-python/lib/bx/bitset_utils.py
external/bx-python/lib/bx/filter.py
external/bx-python/lib/bx/gene_reader.py
external/bx-python/lib/bx/interval_index_file.py
external/bx-python/lib/bx/interval_index_file_tests.py
external/bx-python/lib/bx/seqmapping.py
external/bx-python/lib/bx/seqmapping_tests.py
external/bx-python/lib/bx/wiggle.py
external/bx-python/lib/bx/wiggle_tests.py
external/bx-python/lib/bx/align/__init__.py
external/bx-python/lib/bx/align/_core.c
external/bx-python/lib/bx/align/_core.pyx
external/bx-python/lib/bx/align/_epo.c
external/bx-python/lib/bx/align/_epo.pyx
external/bx-python/lib/bx/align/axt.py
external/bx-python/lib/bx/align/core.py
external/bx-python/lib/bx/align/epo.py
external/bx-python/lib/bx/align/epo_tests.py
external/bx-python/lib/bx/align/lav.py
external/bx-python/lib/bx/align/lav_tests.py
external/bx-python/lib/bx/align/maf.py
external/bx-python/lib/bx/align/maf_tests.py
external/bx-python/lib/bx/align/score.py
external/bx-python/lib/bx/align/score_tests.py
external/bx-python/lib/bx/align/sitemask/__init__.py
external/bx-python/lib/bx/align/sitemask/_cpg.c
external/bx-python/lib/bx/align/sitemask/_cpg.pyx
external/bx-python/lib/bx/align/sitemask/core.py
external/bx-python/lib/bx/align/sitemask/cpg.py
external/bx-python/lib/bx/align/sitemask/find_cpg.c
external/bx-python/lib/bx/align/sitemask/find_cpg.h
external/bx-python/lib/bx/align/sitemask/quality.py
external/bx-python/lib/bx/align/sitemask/sitemask_tests.py
external/bx-python/lib/bx/align/tools/__init__.py
external/bx-python/lib/bx/align/tools/chop.py
external/bx-python/lib/bx/align/tools/fuse.py
external/bx-python/lib/bx/align/tools/thread.py
external/bx-python/lib/bx/align/tools/tile.py
external/bx-python/lib/bx/arrays/__init__.py
external/bx-python/lib/bx/arrays/array_tree.c
external/bx-python/lib/bx/arrays/array_tree.pyx
external/bx-python/lib/bx/arrays/array_tree_tests.py
external/bx-python/lib/bx/arrays/bed.c
external/bx-python/lib/bx/arrays/bed.pyx
external/bx-python/lib/bx/arrays/wiggle.c
external/bx-python/lib/bx/arrays/wiggle.pxd
external/bx-python/lib/bx/arrays/wiggle.pyx
external/bx-python/lib/bx/bbi/__init__.py
external/bx-python/lib/bx/bbi/bbi_file.c
external/bx-python/lib/bx/bbi/bbi_file.pxd
external/bx-python/lib/bx/bbi/bbi_file.pyx
external/bx-python/lib/bx/bbi/bigbed_file.c
external/bx-python/lib/bx/bbi/bigbed_file.pyx
external/bx-python/lib/bx/bbi/bigwig_file.c
external/bx-python/lib/bx/bbi/bigwig_file.pyx
external/bx-python/lib/bx/bbi/bigwig_tests.py
external/bx-python/lib/bx/bbi/bpt_file.c
external/bx-python/lib/bx/bbi/bpt_file.pxd
external/bx-python/lib/bx/bbi/bpt_file.pyx
external/bx-python/lib/bx/bbi/cirtree_file.c
external/bx-python/lib/bx/bbi/cirtree_file.pxd
external/bx-python/lib/bx/bbi/cirtree_file.pyx
external/bx-python/lib/bx/bbi/types.pxd
external/bx-python/lib/bx/cookbook/__init__.py
external/bx-python/lib/bx/cookbook/argparse.py
external/bx-python/lib/bx/cookbook/attribute.py
external/bx-python/lib/bx/cookbook/doc_optparse.py
external/bx-python/lib/bx/cookbook/progress_bar.py
external/bx-python/lib/bx/intervals/__init__.py
external/bx-python/lib/bx/intervals/cluster.c
external/bx-python/lib/bx/intervals/cluster.pyx
external/bx-python/lib/bx/intervals/cluster_tests.py
external/bx-python/lib/bx/intervals/intersection.c
external/bx-python/lib/bx/intervals/intersection.pyx
external/bx-python/lib/bx/intervals/intersection_tests.py
external/bx-python/lib/bx/intervals/io.py
external/bx-python/lib/bx/intervals/random_intervals.py
external/bx-python/lib/bx/intervals/operations/__init__.py
external/bx-python/lib/bx/intervals/operations/base_coverage.py
external/bx-python/lib/bx/intervals/operations/complement.py
external/bx-python/lib/bx/intervals/operations/concat.py
external/bx-python/lib/bx/intervals/operations/coverage.py
external/bx-python/lib/bx/intervals/operations/find_clusters.py
external/bx-python/lib/bx/intervals/operations/intersect.py
external/bx-python/lib/bx/intervals/operations/join.py
external/bx-python/lib/bx/intervals/operations/merge.py
external/bx-python/lib/bx/intervals/operations/quicksect.py
external/bx-python/lib/bx/intervals/operations/subtract.py
external/bx-python/lib/bx/intseq/__init__.py
external/bx-python/lib/bx/intseq/ngramcount.c
external/bx-python/lib/bx/intseq/ngramcount.pyx
external/bx-python/lib/bx/misc/__init__.py
external/bx-python/lib/bx/misc/_seekbzip2.c
external/bx-python/lib/bx/misc/_seekbzip2.pyx
external/bx-python/lib/bx/misc/bgzf.c
external/bx-python/lib/bx/misc/bgzf.pyx
external/bx-python/lib/bx/misc/bgzf_tests.py
external/bx-python/lib/bx/misc/binary_file.py
external/bx-python/lib/bx/misc/cdb.py
external/bx-python/lib/bx/misc/cdb_tests.py
external/bx-python/lib/bx/misc/filecache.py
external/bx-python/lib/bx/misc/filecache_tests.py
external/bx-python/lib/bx/misc/readlengths.py
external/bx-python/lib/bx/misc/seekbzip2.py
external/bx-python/lib/bx/misc/seekbzip2_tests.py
external/bx-python/lib/bx/misc/seeklzop.py
external/bx-python/lib/bx/misc/seeklzop_tests.py
external/bx-python/lib/bx/motif/__init__.py
external/bx-python/lib/bx/motif/_pwm.c
external/bx-python/lib/bx/motif/_pwm.pyx
external/bx-python/lib/bx/motif/pwm.py
external/bx-python/lib/bx/motif/pwm_tests.py
external/bx-python/lib/bx/motif/io/__init__.py
external/bx-python/lib/bx/motif/io/transfac.py
external/bx-python/lib/bx/motif/io/transfac_tests.py
external/bx-python/lib/bx/motif/logo/__init__.py
external/bx-python/lib/bx/phylo/__init__.py
external/bx-python/lib/bx/phylo/newick.py
external/bx-python/lib/bx/phylo/newick_tests.py
external/bx-python/lib/bx/phylo/phast.py
external/bx-python/lib/bx/phylo/phast_tests.py
external/bx-python/lib/bx/pwm/__init__.py
external/bx-python/lib/bx/pwm/_position_weight_matrix.c
external/bx-python/lib/bx/pwm/_position_weight_matrix.pyx
external/bx-python/lib/bx/pwm/bed_score_aligned_pwm.py
external/bx-python/lib/bx/pwm/bed_score_aligned_string.py
external/bx-python/lib/bx/pwm/maf_select_motifs.py
external/bx-python/lib/bx/pwm/position_weight_matrix.py
external/bx-python/lib/bx/pwm/pwm_score_maf.py
external/bx-python/lib/bx/pwm/pwm_score_motifs.py
external/bx-python/lib/bx/pwm/pwm_score_positions.py
external/bx-python/lib/bx/pwm/pwm_tests.py
external/bx-python/lib/bx/seq/__init__.py
external/bx-python/lib/bx/seq/_nib.c
external/bx-python/lib/bx/seq/_nib.pyx
external/bx-python/lib/bx/seq/_twobit.c
external/bx-python/lib/bx/seq/_twobit.pyx
external/bx-python/lib/bx/seq/core.py
external/bx-python/lib/bx/seq/fasta.py
external/bx-python/lib/bx/seq/fasta_tests.py
external/bx-python/lib/bx/seq/nib.py
external/bx-python/lib/bx/seq/nib_tests.py
external/bx-python/lib/bx/seq/qdna.py
external/bx-python/lib/bx/seq/qdna_tests.py
external/bx-python/lib/bx/seq/seq.py
external/bx-python/lib/bx/seq/seq_tests.py
external/bx-python/lib/bx/seq/twobit.py
external/bx-python/lib/bx/seq/twobit_tests.py
external/bx-python/lib/bx/tabular/__init__.py
external/bx-python/lib/bx/tabular/io.py
test/test.py