├── .flake8 ├── .git-blame-ignore-revs ├── .github ├── dependabot.yml └── workflows │ ├── deploy.yaml │ └── test.yaml ├── .gitignore ├── .isort.cfg ├── .readthedocs.yaml ├── LICENSE ├── MANIFEST.in ├── README.md ├── doc ├── Makefile ├── make.bat ├── requirements.txt └── source │ ├── conf.py │ ├── index.rst │ └── lib │ ├── bx.align.axt.rst │ ├── bx.align.core.rst │ ├── bx.align.epo.rst │ ├── bx.align.epo_tests.rst │ ├── bx.align.lav.rst │ ├── bx.align.lav_tests.rst │ ├── bx.align.maf.rst │ ├── bx.align.maf_tests.rst │ ├── bx.align.rst │ ├── bx.align.score.rst │ ├── bx.align.score_tests.rst │ ├── bx.align.sitemask.core.rst │ ├── bx.align.sitemask.cpg.rst │ ├── bx.align.sitemask.quality.rst │ ├── bx.align.sitemask.rst │ ├── bx.align.sitemask.sitemask_tests.rst │ ├── bx.align.tools.chop.rst │ ├── bx.align.tools.fuse.rst │ ├── bx.align.tools.rst │ ├── bx.align.tools.thread.rst │ ├── bx.align.tools.tile.rst │ ├── bx.arrays.array_tree.rst │ ├── bx.arrays.array_tree_tests.rst │ ├── bx.arrays.bed.rst │ ├── bx.arrays.rst │ ├── bx.arrays.wiggle.rst │ ├── bx.bbi.bbi_file.rst │ ├── bx.bbi.bigbed_file.rst │ ├── bx.bbi.bigwig_file.rst │ ├── bx.bbi.bigwig_tests.rst │ ├── bx.bbi.bpt_file.rst │ ├── bx.bbi.cirtree_file.rst │ ├── bx.bbi.rst │ ├── bx.binned_array.rst │ ├── bx.binned_array_tests.rst │ ├── bx.bitset.rst │ ├── bx.bitset_builders.rst │ ├── bx.bitset_tests.rst │ ├── bx.bitset_utils.rst │ ├── bx.cookbook.attribute.rst │ ├── bx.cookbook.doc_optparse.rst │ ├── bx.cookbook.rst │ ├── bx.filter.rst │ ├── bx.gene_reader.rst │ ├── bx.interval_index_file.rst │ ├── bx.interval_index_file_tests.rst │ ├── bx.intervals.cluster.rst │ ├── bx.intervals.cluster_tests.rst │ ├── bx.intervals.intersection.rst │ ├── bx.intervals.intersection_tests.rst │ ├── bx.intervals.io.rst │ ├── bx.intervals.operations.base_coverage.rst │ ├── bx.intervals.operations.complement.rst │ ├── bx.intervals.operations.concat.rst │ ├── bx.intervals.operations.coverage.rst │ ├── bx.intervals.operations.find_clusters.rst │ ├── bx.intervals.operations.intersect.rst │ ├── bx.intervals.operations.join.rst │ ├── bx.intervals.operations.merge.rst │ ├── bx.intervals.operations.quicksect.rst │ ├── bx.intervals.operations.rst │ ├── bx.intervals.operations.subtract.rst │ ├── bx.intervals.random_intervals.rst │ ├── bx.intervals.rst │ ├── bx.intseq.ngramcount.rst │ ├── bx.intseq.rst │ ├── bx.misc.bgzf.rst │ ├── bx.misc.bgzf_tests.rst │ ├── bx.misc.binary_file.rst │ ├── bx.misc.cdb.rst │ ├── bx.misc.cdb_tests.rst │ ├── bx.misc.filecache.rst │ ├── bx.misc.filecache_tests.rst │ ├── bx.misc.readlengths.rst │ ├── bx.misc.rst │ ├── bx.misc.seekbzip2.rst │ ├── bx.misc.seekbzip2_tests.rst │ ├── bx.misc.seeklzop.rst │ ├── bx.misc.seeklzop_tests.rst │ ├── bx.motif.io.rst │ ├── bx.motif.io.transfac.rst │ ├── bx.motif.io.transfac_tests.rst │ ├── bx.motif.logo.rst │ ├── bx.motif.pwm.rst │ ├── bx.motif.pwm_tests.rst │ ├── bx.motif.rst │ ├── bx.phylo.newick.rst │ ├── bx.phylo.newick_tests.rst │ ├── bx.phylo.phast.rst │ ├── bx.phylo.phast_tests.rst │ ├── bx.phylo.rst │ ├── bx.pwm.bed_score_aligned_pwm.rst │ ├── bx.pwm.bed_score_aligned_string.rst │ ├── bx.pwm.maf_select_motifs.rst │ ├── bx.pwm.position_weight_matrix.rst │ ├── bx.pwm.pwm_score_maf.rst │ ├── bx.pwm.pwm_score_motifs.rst │ ├── bx.pwm.pwm_score_positions.rst │ ├── bx.pwm.pwm_tests.rst │ ├── bx.pwm.rst │ ├── bx.rst │ ├── bx.seq.core.rst │ ├── bx.seq.fasta.rst │ ├── bx.seq.fasta_tests.rst │ ├── bx.seq.nib.rst │ ├── bx.seq.nib_tests.rst │ ├── bx.seq.qdna.rst │ ├── bx.seq.qdna_tests.rst │ ├── bx.seq.rst │ ├── bx.seq.seq.rst │ ├── bx.seq.seq_tests.rst │ ├── bx.seq.twobit.rst │ ├── bx.seq.twobit_tests.rst │ ├── bx.seqmapping.rst │ ├── bx.seqmapping_tests.rst │ ├── bx.tabular.io.rst │ ├── bx.tabular.rst │ ├── bx.wiggle.rst │ ├── bx.wiggle_tests.rst │ ├── bx_extras.fpconst.rst │ ├── bx_extras.lrucache.rst │ ├── bx_extras.pstat.rst │ ├── bx_extras.rst │ ├── bx_extras.stats.rst │ └── modules.rst ├── lib ├── bx │ ├── __init__.py │ ├── _seqmapping.pyx │ ├── align │ │ ├── __init__.py │ │ ├── _core.pyx │ │ ├── _epo.pyx │ │ ├── axt.py │ │ ├── core.py │ │ ├── epo.py │ │ ├── epo_tests.py │ │ ├── lav.py │ │ ├── lav_tests.py │ │ ├── maf.py │ │ ├── maf_tests.py │ │ ├── score.py │ │ ├── score_tests.py │ │ ├── sitemask │ │ │ ├── __init__.py │ │ │ ├── _cpg.pyx │ │ │ ├── core.py │ │ │ ├── cpg.py │ │ │ ├── find_cpg.c │ │ │ ├── find_cpg.h │ │ │ ├── quality.py │ │ │ └── sitemask_tests.py │ │ └── tools │ │ │ ├── __init__.py │ │ │ ├── chop.py │ │ │ ├── fuse.py │ │ │ ├── thread.py │ │ │ └── tile.py │ ├── arrays │ │ ├── __init__.py │ │ ├── array_tree.pyx │ │ ├── array_tree_tests.py │ │ ├── bed.pyx │ │ ├── wiggle.pxd │ │ └── wiggle.pyx │ ├── bbi │ │ ├── __init__.py │ │ ├── bbi_file.pxd │ │ ├── bbi_file.pyx │ │ ├── bigbed_file.pyx │ │ ├── bigwig_file.pyx │ │ ├── bigwig_tests.py │ │ ├── bpt_file.pxd │ │ ├── bpt_file.pyx │ │ ├── cirtree_file.pxd │ │ ├── cirtree_file.pyx │ │ └── types.pxd │ ├── binned_array.py │ ├── binned_array_tests.py │ ├── bitset.pyx │ ├── bitset_builders.py │ ├── bitset_tests.py │ ├── bitset_utils.py │ ├── cookbook │ │ ├── __init__.py │ │ ├── attribute.py │ │ └── doc_optparse.py │ ├── filter.py │ ├── gene_reader.py │ ├── interval_index_file.py │ ├── interval_index_file_tests.py │ ├── intervals │ │ ├── __init__.py │ │ ├── cluster.pyx │ │ ├── cluster_tests.py │ │ ├── intersection.pyx │ │ ├── intersection_tests.py │ │ ├── io.py │ │ ├── operations │ │ │ ├── __init__.py │ │ │ ├── base_coverage.py │ │ │ ├── complement.py │ │ │ ├── concat.py │ │ │ ├── coverage.py │ │ │ ├── find_clusters.py │ │ │ ├── intersect.py │ │ │ ├── join.py │ │ │ ├── merge.py │ │ │ ├── quicksect.py │ │ │ └── subtract.py │ │ └── random_intervals.py │ ├── intseq │ │ ├── __init__.py │ │ └── ngramcount.pyx │ ├── misc │ │ ├── __init__.py │ │ ├── _seekbzip2.pyx │ │ ├── bgzf.pyx │ │ ├── bgzf_tests.py │ │ ├── binary_file.py │ │ ├── cdb.py │ │ ├── cdb_tests.py │ │ ├── filecache.py │ │ ├── filecache_tests.py │ │ ├── readlengths.py │ │ ├── seekbzip2.py │ │ ├── seekbzip2_tests.py │ │ ├── seeklzop.py │ │ └── seeklzop_tests.py │ ├── motif │ │ ├── __init__.py │ │ ├── _pwm.pyx │ │ ├── io │ │ │ ├── __init__.py │ │ │ ├── transfac.py │ │ │ └── transfac_tests.py │ │ ├── logo │ │ │ ├── __init__.py │ │ │ └── template.ps │ │ ├── pwm.py │ │ └── pwm_tests.py │ ├── phylo │ │ ├── __init__.py │ │ ├── newick.py │ │ ├── newick_tests.py │ │ ├── phast.py │ │ └── phast_tests.py │ ├── pwm │ │ ├── __init__.py │ │ ├── _position_weight_matrix.pyx │ │ ├── bed_score_aligned_pwm.py │ │ ├── bed_score_aligned_string.py │ │ ├── maf_select_motifs.py │ │ ├── position_weight_matrix.py │ │ ├── pwm_score_maf.py │ │ ├── pwm_score_motifs.py │ │ ├── pwm_score_positions.py │ │ └── pwm_tests.py │ ├── seq │ │ ├── __init__.py │ │ ├── _nib.pyx │ │ ├── _twobit.pyx │ │ ├── core.py │ │ ├── fasta.py │ │ ├── fasta_tests.py │ │ ├── nib.py │ │ ├── nib_tests.py │ │ ├── qdna.py │ │ ├── qdna_tests.py │ │ ├── seq.py │ │ ├── seq_tests.py │ │ ├── twobit.py │ │ └── twobit_tests.py │ ├── seqmapping.py │ ├── seqmapping_tests.py │ ├── tabular │ │ ├── __init__.py │ │ └── io.py │ ├── wiggle.py │ └── wiggle_tests.py └── bx_extras │ ├── __init__.py │ ├── fpconst.py │ ├── fpconst_tests.py │ ├── lrucache.py │ ├── pstat.py │ └── stats.py ├── mypy.ini ├── pyproject.toml ├── pytest.ini ├── script_tests ├── base │ └── __init__.py ├── bnMapper_tests.py ├── line_select_tests.py ├── lzop_build_offset_table_tests.py ├── maf_build_index_tests.py ├── maf_chunk_tests.py ├── maf_extract_ranges_indexed_tests.py ├── maf_extract_ranges_tests.py ├── maf_limit_to_species_tests.py ├── maf_select_tests.py └── out_to_chain_tests.py ├── scripts ├── aggregate_scores_in_intervals.py ├── align_print_template.py ├── axt_extract_ranges.py ├── axt_to_fasta.py ├── axt_to_lav.py ├── axt_to_maf.py ├── bed_bigwig_profile.py ├── bed_build_windows.py ├── bed_complement.py ├── bed_count_by_interval.py ├── bed_count_overlapping.py ├── bed_coverage.py ├── bed_coverage_by_interval.py ├── bed_diff_basewise_summary.py ├── bed_extend_to.py ├── bed_intersect.py ├── bed_intersect_basewise.py ├── bed_merge_overlapping.py ├── bed_rand_intersect.py ├── bed_subtract_basewise.py ├── bnMapper.py ├── div_snp_table_chr.py ├── find_in_sorted_file.py ├── gene_fourfold_sites.py ├── get_scores_in_intervals.py ├── int_seqs_to_char_strings.py ├── interval_count_intersections.py ├── interval_join.py ├── lav_to_axt.py ├── lav_to_maf.py ├── line_select.py ├── lzop_build_offset_table.py ├── mMK_bitset.py ├── maf_build_index.py ├── maf_chop.py ├── maf_chunk.py ├── maf_col_counts.py ├── maf_col_counts_all.py ├── maf_count.py ├── maf_covered_ranges.py ├── maf_covered_regions.py ├── maf_div_sites.py ├── maf_drop_overlapping.py ├── maf_extract_chrom_ranges.py ├── maf_extract_ranges.py ├── maf_extract_ranges_indexed.py ├── maf_filter.py ├── maf_filter_max_wc.py ├── maf_gap_frequency.py ├── maf_gc_content.py ├── maf_interval_alignibility.py ├── maf_limit_to_species.py ├── maf_mapping_word_frequency.py ├── maf_mask_cpg.py ├── maf_mean_length_ungapped_piece.py ├── maf_percent_columns_matching.py ├── maf_percent_identity.py ├── maf_print_chroms.py ├── maf_print_scores.py ├── maf_randomize.py ├── maf_region_coverage_by_src.py ├── maf_select.py ├── maf_shuffle_columns.py ├── maf_species_in_all_files.py ├── maf_split_by_src.py ├── maf_thread_for_species.py ├── maf_tile.py ├── maf_tile_2.py ├── maf_tile_2bit.py ├── maf_to_axt.py ├── maf_to_concat_fasta.py ├── maf_to_fasta.py ├── maf_to_int_seqs.py ├── maf_translate_chars.py ├── maf_truncate.py ├── maf_word_frequency.py ├── mask_quality.py ├── nib_chrom_intervals_to_fasta.py ├── nib_intervals_to_fasta.py ├── nib_length.py ├── one_field_per_line.py ├── out_to_chain.py ├── prefix_lines.py ├── pretty_table.py ├── qv_to_bqv.py ├── random_lines.py ├── table_add_column.py ├── table_filter.py ├── tfloc_summary.py ├── ucsc_gene_table_to_intervals.py ├── wiggle_to_array_tree.py ├── wiggle_to_binned_array.py ├── wiggle_to_chr_binned_array.py └── wiggle_to_simple.py ├── setup.py ├── src ├── binBits.c ├── binBits.h ├── bunzip │ ├── micro-bunzip.c │ └── micro-bunzip.h ├── cluster.c ├── cluster.h ├── kent │ ├── bits.c │ ├── bits.h │ ├── common.c │ └── common.h ├── npy_capsule_as_void_ptr.h ├── pwm_utils.c ├── pwm_utils.h └── samtools │ ├── bgzf.c │ ├── bgzf.h │ └── khash.h ├── test_data ├── bbi_tests │ ├── make_expectation.sh │ ├── test.bw │ ├── test.expectation │ ├── test.regions │ └── test.wig ├── bgzf_tests │ ├── test.txt │ └── test.txt.gz ├── epo_tests │ ├── epo_547_hs_mm_12way_mammals_65.chain │ ├── epo_547_hs_mm_12way_mammals_65.out │ ├── hg19.chrom.sizes │ ├── hg19.mm9.rBest.chain.gz │ ├── hg19_one_peak.bed │ ├── hg19_one_peak.mapped.bed │ ├── hpeaks.bed │ ├── hpeaks.mapped.bed12 │ ├── hpeaks.mapped.bed4 │ ├── hpeaks.mapped.nopeak2.bed4 │ └── mm9.chrom.sizes ├── lav_tests │ ├── apple.fa │ ├── apple_orange.lav │ ├── orange.fa │ └── orange.nib ├── maf_tests │ ├── chunk1 │ │ ├── 000000000.maf │ │ ├── 000000001.maf │ │ ├── 000000002.maf │ │ ├── 000000003.maf │ │ ├── 000000004.maf │ │ ├── 000000005.maf │ │ ├── 000000006.maf │ │ ├── 000000007.maf │ │ └── intervals.txt │ ├── chunk1000 │ │ ├── 000000000.maf │ │ └── intervals.txt │ ├── dcking_ghp074.bed │ ├── dcking_ghp074.maf │ ├── empty.maf │ ├── hg18.bed │ ├── mm10_chr12.bed │ ├── mm10_chr12_lessspe.maf │ ├── mm10_chr12_lessspe.maf.index │ ├── mm10_chr12_lessspe_one_selected.maf │ ├── mm10_chr12_lessspe_onlymouse_cow_elephant.maf │ ├── mm10_chr12_slice.maf │ ├── mm10_chr12_slice2.maf │ ├── mm8_chr7_tiny.maf │ ├── mm8_chr7_tiny.maf.bz2 │ ├── mm8_chr7_tiny.maf.bz2t │ ├── mm8_chr7_tiny.maf.index │ ├── mm8_chr7_tiny.maf.lzo │ ├── mm8_chr7_tiny.maf.lzot │ ├── mm8_chr7_tiny_last_selected.maf │ ├── mm8_chr7_tiny_mm8_ind.maf │ ├── mm8_chr7_tiny_mm8_ind.maf.index │ ├── mm8_chr7_tiny_no_index.maf │ ├── mm8_chr7_tiny_only_mouse_rat.maf │ └── test_hg18.maf └── seq_tests │ ├── test.2bit │ ├── test.fa │ ├── 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