LICENSE
MANIFEST.in
README.md
setup.cfg
setup.py
lib/psyco_full.py
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.h
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/fpconst_tests.py
lib/bx_extras/lrucache.py
lib/bx_extras/pstat.py
lib/bx_extras/pyparsing.py
lib/bx_extras/stats.py
lib/bx_python.egg-info/PKG-INFO
lib/bx_python.egg-info/SOURCES.txt
lib/bx_python.egg-info/dependency_links.txt
lib/bx_python.egg-info/not-zip-safe
lib/bx_python.egg-info/requires.txt
lib/bx_python.egg-info/top_level.txt
scripts/aggregate_scores_in_intervals.py
scripts/align_print_template.py
scripts/axt_extract_ranges.py
scripts/axt_to_fasta.py
scripts/axt_to_lav.py
scripts/axt_to_maf.py
scripts/bed_bigwig_profile.py
scripts/bed_build_windows.py
scripts/bed_complement.py
scripts/bed_count_by_interval.py
scripts/bed_count_overlapping.py
scripts/bed_coverage.py
scripts/bed_coverage_by_interval.py
scripts/bed_diff_basewise_summary.py
scripts/bed_extend_to.py
scripts/bed_intersect.py
scripts/bed_intersect_basewise.py
scripts/bed_merge_overlapping.py
scripts/bed_rand_intersect.py
scripts/bed_subtract_basewise.py
scripts/bnMapper.py
scripts/div_snp_table_chr.py
scripts/find_in_sorted_file.py
scripts/gene_fourfold_sites.py
scripts/get_scores_in_intervals.py
scripts/int_seqs_to_char_strings.py
scripts/interval_count_intersections.py
scripts/interval_join.py
scripts/lav_to_axt.py
scripts/lav_to_maf.py
scripts/line_select.py
scripts/lzop_build_offset_table.py
scripts/mMK_bitset.py
scripts/maf_build_index.py
scripts/maf_chop.py
scripts/maf_chunk.py
scripts/maf_col_counts.py
scripts/maf_col_counts_all.py
scripts/maf_count.py
scripts/maf_covered_ranges.py
scripts/maf_covered_regions.py
scripts/maf_div_sites.py
scripts/maf_drop_overlapping.py
scripts/maf_extract_chrom_ranges.py
scripts/maf_extract_ranges.py
scripts/maf_extract_ranges_indexed.py
scripts/maf_filter.py
scripts/maf_filter_max_wc.py
scripts/maf_gap_frequency.py
scripts/maf_gc_content.py
scripts/maf_interval_alignibility.py
scripts/maf_limit_to_species.py
scripts/maf_mapping_word_frequency.py
scripts/maf_mask_cpg.py
scripts/maf_mean_length_ungapped_piece.py
scripts/maf_percent_columns_matching.py
scripts/maf_percent_identity.py
scripts/maf_print_chroms.py
scripts/maf_print_scores.py
scripts/maf_randomize.py
scripts/maf_region_coverage_by_src.py
scripts/maf_select.py
scripts/maf_shuffle_columns.py
scripts/maf_species_in_all_files.py
scripts/maf_split_by_src.py
scripts/maf_thread_for_species.py
scripts/maf_tile.py
scripts/maf_tile_2.py
scripts/maf_tile_2bit.py
scripts/maf_to_axt.py
scripts/maf_to_concat_fasta.py
scripts/maf_to_fasta.py
scripts/maf_to_int_seqs.py
scripts/maf_translate_chars.py
scripts/maf_truncate.py
scripts/maf_word_frequency.py
scripts/mask_quality.py
scripts/nib_chrom_intervals_to_fasta.py
scripts/nib_intervals_to_fasta.py
scripts/nib_length.py
scripts/one_field_per_line.py
scripts/out_to_chain.py
scripts/prefix_lines.py
scripts/pretty_table.py
scripts/qv_to_bqv.py
scripts/random_lines.py
scripts/table_add_column.py
scripts/table_filter.py
scripts/tfloc_summary.py
scripts/ucsc_gene_table_to_intervals.py
scripts/wiggle_to_array_tree.py
scripts/wiggle_to_binned_array.py
scripts/wiggle_to_chr_binned_array.py
scripts/wiggle_to_simple.py
src/binBits.c
src/binBits.h
src/cluster.c
src/cluster.h
src/npy_capsule_as_void_ptr.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