../psyco_full.py ../bx_extras/fpconst.py ../bx_extras/stats.py ../bx_extras/pstat.py ../bx_extras/__init__.py ../bx_extras/lrucache.py ../bx_extras/pyparsing.py ../bx/wiggle.py ../bx/gene_reader.py ../bx/interval_index_file.py ../bx/interval_index_file_tests.py ../bx/wiggle_tests.py ../bx/binned_array_tests.py ../bx/bitset_builders.py ../bx/binned_array.py ../bx/filter.py ../bx/bitset_tests.py ../bx/seqmapping_tests.py ../bx/__init__.py ../bx/bitset_utils.py ../bx/seqmapping.py ../bx/cookbook/attribute.py ../bx/cookbook/argparse.py ../bx/cookbook/__init__.py ../bx/cookbook/doc_optparse.py ../bx/cookbook/progress_bar.py ../bx/intseq/__init__.py ../bx/misc/filecache.py ../bx/misc/binary_file.py ../bx/misc/seeklzop_tests.py ../bx/misc/bgzf_tests.py ../bx/misc/seekbzip2_tests.py ../bx/misc/filecache_tests.py ../bx/misc/seeklzop.py ../bx/misc/readlengths.py ../bx/misc/__init__.py ../bx/misc/seekbzip2.py ../bx/misc/cdb_tests.py ../bx/misc/cdb.py ../bx/pwm/pwm_score_motifs.py ../bx/pwm/maf_select_motifs.py ../bx/pwm/pwm_score_maf.py ../bx/pwm/position_weight_matrix.py ../bx/pwm/pwm_score_positions.py ../bx/pwm/bed_score_aligned_pwm.py ../bx/pwm/bed_score_aligned_string.py ../bx/pwm/__init__.py ../bx/pwm/pwm_tests.py ../bx/motif/__init__.py ../bx/motif/pwm_tests.py ../bx/motif/pwm.py ../bx/seq/qdna_tests.py ../bx/seq/twobit_tests.py ../bx/seq/fasta.py ../bx/seq/seq_tests.py ../bx/seq/fasta_tests.py ../bx/seq/nib.py ../bx/seq/__init__.py ../bx/seq/qdna.py ../bx/seq/core.py ../bx/seq/seq.py ../bx/seq/nib_tests.py ../bx/seq/twobit.py ../bx/bbi/__init__.py ../bx/bbi/bigwig_tests.py ../bx/align/lav_tests.py ../bx/align/epo.py ../bx/align/maf.py ../bx/align/epo_tests.py ../bx/align/__init__.py ../bx/align/maf_tests.py ../bx/align/score.py ../bx/align/axt.py ../bx/align/core.py ../bx/align/score_tests.py ../bx/align/lav.py ../bx/arrays/array_tree_tests.py ../bx/arrays/__init__.py ../bx/phylo/newick.py ../bx/phylo/newick_tests.py ../bx/phylo/phast_tests.py ../bx/phylo/__init__.py ../bx/phylo/phast.py ../bx/intervals/intersection_tests.py ../bx/intervals/random_intervals.py ../bx/intervals/cluster_tests.py ../bx/intervals/__init__.py ../bx/intervals/io.py ../bx/tabular/__init__.py ../bx/tabular/io.py ../bx/motif/io/transfac.py ../bx/motif/io/transfac_tests.py ../bx/motif/io/__init__.py ../bx/motif/logo/__init__.py ../bx/align/sitemask/cpg.py ../bx/align/sitemask/__init__.py ../bx/align/sitemask/sitemask_tests.py ../bx/align/sitemask/core.py ../bx/align/sitemask/quality.py ../bx/align/tools/fuse.py ../bx/align/tools/thread.py ../bx/align/tools/chop.py ../bx/align/tools/tile.py ../bx/align/tools/__init__.py ../bx/intervals/operations/quicksect.py ../bx/intervals/operations/subtract.py ../bx/intervals/operations/base_coverage.py ../bx/intervals/operations/find_clusters.py ../bx/intervals/operations/join.py ../bx/intervals/operations/__init__.py ../bx/intervals/operations/merge.py ../bx/intervals/operations/intersect.py ../bx/intervals/operations/coverage.py ../bx/intervals/operations/complement.py ../bx/intervals/operations/concat.py ../bx/motif/logo/template.ps ../psyco_full.pyc ../bx_extras/fpconst.pyc ../bx_extras/stats.pyc ../bx_extras/pstat.pyc ../bx_extras/__init__.pyc ../bx_extras/lrucache.pyc ../bx_extras/pyparsing.pyc ../bx/wiggle.pyc ../bx/gene_reader.pyc ../bx/interval_index_file.pyc ../bx/interval_index_file_tests.pyc ../bx/wiggle_tests.pyc ../bx/binned_array_tests.pyc ../bx/bitset_builders.pyc ../bx/binned_array.pyc ../bx/filter.pyc ../bx/bitset_tests.pyc ../bx/seqmapping_tests.pyc ../bx/__init__.pyc ../bx/bitset_utils.pyc ../bx/seqmapping.pyc ../bx/cookbook/attribute.pyc ../bx/cookbook/argparse.pyc ../bx/cookbook/__init__.pyc ../bx/cookbook/doc_optparse.pyc ../bx/cookbook/progress_bar.pyc ../bx/intseq/__init__.pyc ../bx/misc/filecache.pyc ../bx/misc/binary_file.pyc ../bx/misc/seeklzop_tests.pyc ../bx/misc/bgzf_tests.pyc ../bx/misc/seekbzip2_tests.pyc ../bx/misc/filecache_tests.pyc ../bx/misc/seeklzop.pyc ../bx/misc/readlengths.pyc ../bx/misc/__init__.pyc ../bx/misc/seekbzip2.pyc ../bx/misc/cdb_tests.pyc ../bx/misc/cdb.pyc ../bx/pwm/pwm_score_motifs.pyc ../bx/pwm/maf_select_motifs.pyc ../bx/pwm/pwm_score_maf.pyc ../bx/pwm/position_weight_matrix.pyc ../bx/pwm/pwm_score_positions.pyc ../bx/pwm/bed_score_aligned_pwm.pyc ../bx/pwm/bed_score_aligned_string.pyc ../bx/pwm/__init__.pyc ../bx/pwm/pwm_tests.pyc ../bx/motif/__init__.pyc ../bx/motif/pwm_tests.pyc ../bx/motif/pwm.pyc ../bx/seq/qdna_tests.pyc ../bx/seq/twobit_tests.pyc ../bx/seq/fasta.pyc ../bx/seq/seq_tests.pyc ../bx/seq/fasta_tests.pyc ../bx/seq/nib.pyc ../bx/seq/__init__.pyc ../bx/seq/qdna.pyc ../bx/seq/core.pyc ../bx/seq/seq.pyc ../bx/seq/nib_tests.pyc ../bx/seq/twobit.pyc ../bx/bbi/__init__.pyc ../bx/bbi/bigwig_tests.pyc ../bx/align/lav_tests.pyc ../bx/align/epo.pyc ../bx/align/maf.pyc ../bx/align/epo_tests.pyc ../bx/align/__init__.pyc ../bx/align/maf_tests.pyc ../bx/align/score.pyc ../bx/align/axt.pyc ../bx/align/core.pyc ../bx/align/score_tests.pyc ../bx/align/lav.pyc ../bx/arrays/array_tree_tests.pyc ../bx/arrays/__init__.pyc ../bx/phylo/newick.pyc ../bx/phylo/newick_tests.pyc ../bx/phylo/phast_tests.pyc ../bx/phylo/__init__.pyc ../bx/phylo/phast.pyc ../bx/intervals/intersection_tests.pyc ../bx/intervals/random_intervals.pyc ../bx/intervals/cluster_tests.pyc ../bx/intervals/__init__.pyc ../bx/intervals/io.pyc ../bx/tabular/__init__.pyc ../bx/tabular/io.pyc ../bx/motif/io/transfac.pyc ../bx/motif/io/transfac_tests.pyc ../bx/motif/io/__init__.pyc ../bx/motif/logo/__init__.pyc ../bx/align/sitemask/cpg.pyc ../bx/align/sitemask/__init__.pyc ../bx/align/sitemask/sitemask_tests.pyc ../bx/align/sitemask/core.pyc ../bx/align/sitemask/quality.pyc ../bx/align/tools/fuse.pyc ../bx/align/tools/thread.pyc ../bx/align/tools/chop.pyc ../bx/align/tools/tile.pyc ../bx/align/tools/__init__.pyc ../bx/intervals/operations/quicksect.pyc ../bx/intervals/operations/subtract.pyc ../bx/intervals/operations/base_coverage.pyc ../bx/intervals/operations/find_clusters.pyc ../bx/intervals/operations/join.pyc ../bx/intervals/operations/__init__.pyc ../bx/intervals/operations/merge.pyc ../bx/intervals/operations/intersect.pyc ../bx/intervals/operations/coverage.pyc ../bx/intervals/operations/complement.pyc ../bx/intervals/operations/concat.pyc ../bx/bitset.so ../bx/intervals/intersection.so ../bx/align/_core.so ../bx/seq/_nib.so ../bx/seq/_twobit.so ../bx/_seqmapping.so ../bx/misc/bgzf.so ../bx/intervals/cluster.so ../bx/pwm/_position_weight_matrix.so ../bx/motif/_pwm.so ../bx/arrays/array_tree.so ../bx/bbi/bpt_file.so ../bx/bbi/cirtree_file.so ../bx/bbi/bbi_file.so ../bx/bbi/bigwig_file.so ../bx/bbi/bigbed_file.so ../bx/align/_epo.so ../bx/arrays/bed.so ../bx/arrays/wiggle.so ../bx/align/sitemask/_cpg.so ../bx/intseq/ngramcount.so ../bx/misc/_seekbzip2.so dependency_links.txt SOURCES.txt not-zip-safe top_level.txt PKG-INFO ../../../../bin/bnMapper.py ../../../../bin/ucsc_gene_table_to_intervals.py ../../../../bin/maf_extract_ranges_indexed.py ../../../../bin/maf_to_fasta.py ../../../../bin/interval_join.py ../../../../bin/maf_filter.py ../../../../bin/maf_to_axt.py ../../../../bin/wiggle_to_chr_binned_array.py ../../../../bin/maf_col_counts.py ../../../../bin/lav_to_axt.py ../../../../bin/interval_count_intersections.py ../../../../bin/wiggle_to_array_tree.py ../../../../bin/out_to_chain.py ../../../../bin/lzop_build_offset_table.py ../../../../bin/maf_tile_2.py ../../../../bin/maf_percent_columns_matching.py ../../../../bin/nib_chrom_intervals_to_fasta.py ../../../../bin/maf_build_index.py ../../../../bin/maf_col_counts_all.py ../../../../bin/maf_region_coverage_by_src.py ../../../../bin/maf_truncate.py ../../../../bin/random_lines.py ../../../../bin/maf_drop_overlapping.py ../../../../bin/maf_translate_chars.py ../../../../bin/line_select.py ../../../../bin/maf_filter_max_wc.py ../../../../bin/maf_word_frequency.py ../../../../bin/mask_quality.py ../../../../bin/maf_covered_regions.py ../../../../bin/maf_tile_2bit.py ../../../../bin/maf_tile.py ../../../../bin/maf_select.py ../../../../bin/qv_to_bqv.py ../../../../bin/maf_randomize.py ../../../../bin/wiggle_to_binned_array.py ../../../../bin/maf_mean_length_ungapped_piece.py ../../../../bin/align_print_template.py ../../../../bin/maf_print_chroms.py ../../../../bin/maf_extract_ranges.py ../../../../bin/bed_extend_to.py ../../../../bin/bed_intersect.py ../../../../bin/maf_gc_content.py ../../../../bin/get_scores_in_intervals.py ../../../../bin/maf_to_concat_fasta.py ../../../../bin/mMK_bitset.py ../../../../bin/maf_species_in_all_files.py ../../../../bin/aggregate_scores_in_intervals.py ../../../../bin/maf_interval_alignibility.py ../../../../bin/lav_to_maf.py ../../../../bin/one_field_per_line.py ../../../../bin/bed_count_overlapping.py ../../../../bin/maf_mapping_word_frequency.py ../../../../bin/find_in_sorted_file.py ../../../../bin/maf_shuffle_columns.py ../../../../bin/maf_mask_cpg.py ../../../../bin/axt_to_maf.py ../../../../bin/maf_split_by_src.py ../../../../bin/maf_chunk.py ../../../../bin/maf_percent_identity.py ../../../../bin/bed_coverage.py ../../../../bin/maf_div_sites.py ../../../../bin/bed_bigwig_profile.py ../../../../bin/maf_gap_frequency.py ../../../../bin/bed_merge_overlapping.py ../../../../bin/maf_limit_to_species.py ../../../../bin/maf_thread_for_species.py ../../../../bin/prefix_lines.py ../../../../bin/table_add_column.py ../../../../bin/bed_intersect_basewise.py ../../../../bin/nib_intervals_to_fasta.py ../../../../bin/nib_length.py ../../../../bin/int_seqs_to_char_strings.py ../../../../bin/maf_extract_chrom_ranges.py ../../../../bin/axt_to_lav.py ../../../../bin/bed_subtract_basewise.py ../../../../bin/bed_diff_basewise_summary.py ../../../../bin/maf_chop.py ../../../../bin/maf_covered_ranges.py ../../../../bin/div_snp_table_chr.py ../../../../bin/axt_extract_ranges.py ../../../../bin/wiggle_to_simple.py ../../../../bin/maf_print_scores.py ../../../../bin/maf_count.py ../../../../bin/maf_to_int_seqs.py ../../../../bin/bed_coverage_by_interval.py ../../../../bin/pretty_table.py ../../../../bin/gene_fourfold_sites.py ../../../../bin/tfloc_summary.py ../../../../bin/bed_count_by_interval.py ../../../../bin/axt_to_fasta.py ../../../../bin/bed_build_windows.py ../../../../bin/table_filter.py ../../../../bin/bed_complement.py ../../../../bin/bed_rand_intersect.py