Index A | B | C | E | F | G | I | L | M | N | O | P | R | S | T | U A add_gene_annotations() (in module ontmont.plot) add_sv_legend_to_axes() (in module ontmont.plot) align_two_sequences() (in module ontmont.irs) B Breakpoint (class in ontmont.datatypes) BreakpointChain (class in ontmont.datatypes) BreakpointPair (class in ontmont.datatypes) C calc_distance_score() (in module ontmont.irs) calc_pval_bilateral_ir() (in module ontmont.irs) calc_pval_holliday() (in module ontmont.irs) calc_pval_onesided_ir() (in module ontmont.irs) calc_pval_segmental_ir() (in module ontmont.irs) chroms (ontmont.datatypes.Breakpoint attribute) convert_tupleproxy_to_pyranges() (in module ontmont.plot) E enumerate_breakpoints() (in module ontmont.utils) extract_cigar_field() (ontmont.datatypes.SplitAlignment method) extract_split_alignments() (in module ontmont.collect) (in module ontmont.utils) extract_vaf_from_annotated_sv_table() (in module ontmont.plot) F filter_breakpoints_at_contig_ends() (in module ontmont.utils) filter_sv_by_clone() (in module ontmont.process) filter_sv_with_breakpoint_at_contig_ends() (in module ontmont.utils) find_presence_of_matching_sv() (in module ontmont.collect) fix_coordinate_xticklabels() (in module ontmont.plot) fix_lower_support_coordinates() (in module ontmont.collect) fix_yticks_with_integers() (in module ontmont.plot) G get_best_holliday_junctions() (in module ontmont.irs) get_best_ir_within_breakpoints() (in module ontmont.irs) get_best_ir_within_segment() (in module ontmont.irs) get_best_onesided_ir() (in module ontmont.irs) get_breakpoint_pair_seq_data() (in module ontmont.irs) get_breakpoint_seqs() (in module ontmont.datatypes) (ontmont.datatypes.Breakpoint method) get_breakpoint_support_from_bundle() (in module ontmont.collect) get_chrom_xlims() (in module ontmont.plot) get_chromosomes_from_bundle() (in module ontmont.plot) get_chromosomes_to_process() (in module ontmont.utils) get_cigar_tuples() (ontmont.datatypes.SplitAlignment static method) get_cn_blocks_for_read_xlim() (in module ontmont.plot) get_edgecolor() (in module ontmont.plot) get_gene_repr_exons() (in module ontmont.plot) get_list() (ontmont.datatypes.Segments method) (ontmont.datatypes.Transitions method) get_normalized_sv() (in module ontmont.collect) get_onesided_ir() (in module ontmont.irs) get_repr_transcript_id() (in module ontmont.plot) get_secondaries() (in module ontmont.utils) get_segments() (ontmont.datatypes.BreakpointChain method) get_sv_table_chroms() (in module ontmont.plot) get_svtype() (in module ontmont.collect) get_transcript_exons() (in module ontmont.plot) get_transitions() (ontmont.datatypes.BreakpointChain method) get_unique_sv_with_support() (in module ontmont.plot) I is_breakpoints_not_sorted() (in module ontmont.utils) is_holliday_junction() (in module ontmont.irs) is_overlap() (in module ontmont.plot) L long_samples (ontmont.datatypes.Sample attribute) M make_axes_for_breakpoints() (in module ontmont.plot) make_brk_supports() (in module ontmont.bundle) make_brk_table() (in module ontmont.bundle) make_brks_bundle() (in module ontmont.bundle) (in module ontmont.collect) make_seg_table() (in module ontmont.bundle) make_spline_coordinates() (in module ontmont.plot) make_split_read_table() (in module ontmont.utils) make_tra_table() (in module ontmont.bundle) make_tumor_sv_table() (in module ontmont.collect) map_similar_coordinate_to_higher_rank() (in module ontmont.collect) merge_cn_segments() (in module ontmont.process) module ontmont ontmont.bundle ontmont.cli ontmont.collect ontmont.datatypes ontmont.irs ontmont.plot ontmont.process ontmont.utils N normalize_sv_table() (in module ontmont.collect) O ontmont module ontmont.bundle module ontmont.cli module ontmont.collect module ontmont.datatypes module ontmont.irs module ontmont.plot module ontmont.process module ontmont.utils module overlaps() (in module ontmont.irs) P parse_gtf_region() (in module ontmont.plot) plot_cn_on_axes() (in module ontmont.plot) plot_gene_annotations() (in module ontmont.plot) plot_jabba_cn() (in module ontmont.plot) plot_quasijabba() (in module ontmont.plot) plot_segments_on_axes() (in module ontmont.plot) plot_sv_lines_on_cn() (in module ontmont.plot) plot_svs_to_cn_segments() (in module ontmont.plot) plot_transition_on_axes() (in module ontmont.plot) plot_vaf_cn_sv_for_reads() (in module ontmont.plot) plot_vaf_on_axes() (in module ontmont.plot) pull_breakpoints_from_bam_files() (in module ontmont.collect) pull_breakpoints_from_reads_in_sv_regions() (in module ontmont.collect) pull_sv_supporting_reads_from_bundle() (in module ontmont.collect) R remove_duplicates_from_tra_table() (in module ontmont.utils) reverse_complement() (in module ontmont.utils) S Sample (class in ontmont.datatypes) sample2group (ontmont.datatypes.Sample attribute) sample2short (ontmont.datatypes.Sample attribute) Segments (class in ontmont.datatypes) shuffle_seq() (in module ontmont.utils) SplitAlignment (class in ontmont.datatypes) T Transitions (class in ontmont.datatypes) U update_blocks_and_reset_prev() (in module ontmont.process)