lib/bx/_seqmapping.pyx | 2 1 + 1 - 0 !
lib/bx/align/_epo.pyx | 4 2 + 2 - 0 !
lib/bx/align/epo.py | 2 1 + 1 - 0 !
lib/bx/align/epo_tests.py | 4 2 + 2 - 0 !
scripts/bnMapper.py | 4 2 + 2 - 0 !
scripts/maf_tile_2.py | 2 1 + 1 - 0 !
scripts/maf_tile_2bit.py | 2 1 + 1 - 0 !
scripts/mask_quality.py | 2 1 + 1 - 0 !
8 files changed, 11 insertions(+), 11 deletions(-)

 fix typos

lib/bx/intervals/operations/subtract.py | 2 1 + 1 - 0 !
lib/bx/pwm/bed_score_aligned_pwm.py | 2 1 + 1 - 0 !
lib/bx/pwm/bed_score_aligned_string.py | 2 1 + 1 - 0 !
lib/bx/pwm/maf_select_motifs.py | 2 1 + 1 - 0 !
lib/bx/pwm/position_weight_matrix.py | 2 1 + 1 - 0 !
lib/bx/pwm/pwm_score_maf.py | 2 1 + 1 - 0 !
lib/bx/pwm/pwm_score_motifs.py | 2 1 + 1 - 0 !
lib/bx/pwm/pwm_score_positions.py | 2 1 + 1 - 0 !
scripts/aggregate_scores_in_intervals.py | 2 1 + 1 - 0 !
scripts/align_print_template.py | 2 1 + 1 - 0 !
scripts/axt_extract_ranges.py | 2 1 + 1 - 0 !
scripts/axt_to_fasta.py | 2 1 + 1 - 0 !
scripts/axt_to_lav.py | 2 1 + 1 - 0 !
scripts/axt_to_maf.py | 2 1 + 1 - 0 !
scripts/bed_bigwig_profile.py | 2 1 + 1 - 0 !
scripts/bed_build_windows.py | 2 1 + 1 - 0 !
scripts/bed_complement.py | 2 1 + 1 - 0 !
scripts/bed_count_by_interval.py | 2 1 + 1 - 0 !
scripts/bed_count_overlapping.py | 2 1 + 1 - 0 !
scripts/bed_coverage.py | 2 1 + 1 - 0 !
scripts/bed_coverage_by_interval.py | 2 1 + 1 - 0 !
scripts/bed_diff_basewise_summary.py | 2 1 + 1 - 0 !
scripts/bed_extend_to.py | 2 1 + 1 - 0 !
scripts/bed_intersect.py | 2 1 + 1 - 0 !
scripts/bed_intersect_basewise.py | 2 1 + 1 - 0 !
scripts/bed_merge_overlapping.py | 2 1 + 1 - 0 !
scripts/bed_rand_intersect.py | 2 1 + 1 - 0 !
scripts/bed_subtract_basewise.py | 2 1 + 1 - 0 !
scripts/bnMapper.py | 2 1 + 1 - 0 !
scripts/div_snp_table_chr.py | 2 1 + 1 - 0 !
scripts/find_in_sorted_file.py | 2 1 + 1 - 0 !
scripts/get_scores_in_intervals.py | 2 1 + 1 - 0 !
scripts/int_seqs_to_char_strings.py | 2 1 + 1 - 0 !
scripts/interval_count_intersections.py | 2 1 + 1 - 0 !
scripts/interval_join.py | 2 1 + 1 - 0 !
scripts/lav_to_axt.py | 2 1 + 1 - 0 !
scripts/lav_to_maf.py | 2 1 + 1 - 0 !
scripts/line_select.py | 2 1 + 1 - 0 !
scripts/lzop_build_offset_table.py | 2 1 + 1 - 0 !
scripts/mMK_bitset.py | 2 1 + 1 - 0 !
scripts/maf_build_index.py | 2 1 + 1 - 0 !
scripts/maf_chop.py | 2 1 + 1 - 0 !
scripts/maf_chunk.py | 2 1 + 1 - 0 !
scripts/maf_col_counts.py | 2 1 + 1 - 0 !
scripts/maf_col_counts_all.py | 2 1 + 1 - 0 !
scripts/maf_count.py | 2 1 + 1 - 0 !
scripts/maf_covered_ranges.py | 2 1 + 1 - 0 !
scripts/maf_covered_regions.py | 2 1 + 1 - 0 !
scripts/maf_div_sites.py | 2 1 + 1 - 0 !
scripts/maf_drop_overlapping.py | 2 1 + 1 - 0 !
scripts/maf_extract_chrom_ranges.py | 2 1 + 1 - 0 !
scripts/maf_extract_ranges.py | 2 1 + 1 - 0 !
scripts/maf_extract_ranges_indexed.py | 2 1 + 1 - 0 !
scripts/maf_filter.py | 2 1 + 1 - 0 !
scripts/maf_filter_max_wc.py | 2 1 + 1 - 0 !
scripts/maf_gap_frequency.py | 2 1 + 1 - 0 !
scripts/maf_gc_content.py | 2 1 + 1 - 0 !
scripts/maf_interval_alignibility.py | 2 1 + 1 - 0 !
scripts/maf_limit_to_species.py | 2 1 + 1 - 0 !
scripts/maf_mapping_word_frequency.py | 2 1 + 1 - 0 !
scripts/maf_mask_cpg.py | 2 1 + 1 - 0 !
scripts/maf_mean_length_ungapped_piece.py | 2 1 + 1 - 0 !
scripts/maf_percent_columns_matching.py | 2 1 + 1 - 0 !
scripts/maf_percent_identity.py | 2 1 + 1 - 0 !
scripts/maf_print_chroms.py | 2 1 + 1 - 0 !
scripts/maf_print_scores.py | 2 1 + 1 - 0 !
scripts/maf_randomize.py | 2 1 + 1 - 0 !
scripts/maf_region_coverage_by_src.py | 2 1 + 1 - 0 !
scripts/maf_select.py | 2 1 + 1 - 0 !
scripts/maf_shuffle_columns.py | 2 1 + 1 - 0 !
scripts/maf_species_in_all_files.py | 2 1 + 1 - 0 !
scripts/maf_split_by_src.py | 2 1 + 1 - 0 !
scripts/maf_thread_for_species.py | 2 1 + 1 - 0 !
scripts/maf_tile.py | 2 1 + 1 - 0 !
scripts/maf_tile_2.py | 2 1 + 1 - 0 !
scripts/maf_tile_2bit.py | 2 1 + 1 - 0 !
scripts/maf_to_axt.py | 2 1 + 1 - 0 !
scripts/maf_to_concat_fasta.py | 2 1 + 1 - 0 !
scripts/maf_to_fasta.py | 2 1 + 1 - 0 !
scripts/maf_to_int_seqs.py | 2 1 + 1 - 0 !
scripts/maf_translate_chars.py | 2 1 + 1 - 0 !
scripts/maf_truncate.py | 2 1 + 1 - 0 !
scripts/maf_word_frequency.py | 2 1 + 1 - 0 !
scripts/mask_quality.py | 2 1 + 1 - 0 !
scripts/nib_chrom_intervals_to_fasta.py | 2 1 + 1 - 0 !
scripts/nib_intervals_to_fasta.py | 2 1 + 1 - 0 !
scripts/nib_length.py | 2 1 + 1 - 0 !
scripts/one_field_per_line.py | 2 1 + 1 - 0 !
scripts/out_to_chain.py | 2 1 + 1 - 0 !
scripts/prefix_lines.py | 2 1 + 1 - 0 !
scripts/pretty_table.py | 2 1 + 1 - 0 !
scripts/qv_to_bqv.py | 2 1 + 1 - 0 !
scripts/random_lines.py | 2 1 + 1 - 0 !
scripts/table_add_column.py | 2 1 + 1 - 0 !
scripts/table_filter.py | 2 1 + 1 - 0 !
scripts/tfloc_summary.py | 2 1 + 1 - 0 !
scripts/ucsc_gene_table_to_intervals.py | 2 1 + 1 - 0 !
scripts/wiggle_to_array_tree.py | 2 1 + 1 - 0 !
scripts/wiggle_to_binned_array.py | 2 1 + 1 - 0 !
scripts/wiggle_to_chr_binned_array.py | 2 1 + 1 - 0 !
scripts/wiggle_to_simple.py | 2 1 + 1 - 0 !
101 files changed, 101 insertions(+), 101 deletions(-)

 fix shebang line to point to python3

lib/bx/interval_index_file.py | 12 7 + 5 - 0 !
1 file changed, 7 insertions(+), 5 deletions(-)

 fix off by one error on 32 bit systems