Index _ | A | B | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | U _ __repr__() (hairloom.BreakpointPair method) (hairloom.datatypes.BreakpointPair method), [1] A aln_cols (hairloom.datatypes.SplitAlignment attribute), [1] aln_segment (hairloom.BreakpointPair attribute) (hairloom.datatypes.BreakpointPair attribute), [1] B Breakpoint (class in hairloom) (class in hairloom.datatypes), [1] BreakpointChain (class in hairloom) (class in hairloom.datatypes), [1] BreakpointPair (class in hairloom) (class in hairloom.datatypes), [1] brk1 (hairloom.BreakpointPair attribute) (hairloom.datatypes.BreakpointPair attribute), [1] brk2 (hairloom.BreakpointPair attribute) (hairloom.datatypes.BreakpointPair attribute), [1] C chrom (hairloom.Breakpoint attribute) (hairloom.datatypes.Breakpoint attribute), [1] chroms (hairloom.Breakpoint attribute), [1] (hairloom.datatypes.Breakpoint attribute), [1], [2], [3] cigar_tuples (hairloom.datatypes.SplitAlignment attribute), [1] cigarstring (hairloom.datatypes.SplitAlignment attribute), [1] clip1 (hairloom.datatypes.SplitAlignment attribute), [1] clip2 (hairloom.datatypes.SplitAlignment attribute), [1] D downstream (hairloom.Breakpoint attribute) (hairloom.datatypes.Breakpoint attribute), [1] E end (hairloom.datatypes.SplitAlignment attribute), [1] enumerate_breakpoints() (in module hairloom.utils), [1] extract_cigar_field() (hairloom.datatypes.SplitAlignment method), [1] extract_read_data() (in module hairloom) (in module hairloom.collect), [1] extract_split_alignments() (in module hairloom.collect), [1] F find_presence_of_matching_sv() (in module hairloom.collect), [1] fix_lower_support_coordinates() (in module hairloom.collect), [1] G get_breakpoint_seqs() (hairloom.Breakpoint method) (hairloom.datatypes.Breakpoint method), [1] (in module hairloom.datatypes), [1] get_breakpoint_support_from_bundle() (in module hairloom.collect), [1] get_cigar_tuples() (hairloom.datatypes.SplitAlignment static method), [1] get_list() (hairloom.datatypes.Segments method), [1] (hairloom.datatypes.Transitions method), [1] (hairloom.Segments method) (hairloom.Transitions method) get_normalized_sv() (in module hairloom.collect), [1] get_secondaries() (in module hairloom.utils), [1] get_svtype() (in module hairloom) (in module hairloom.collect), [1] H hairloom module hairloom.collect module, [1] hairloom.datatypes module, [1] hairloom.utils module, [1] I is_breakpoints_not_sorted() (in module hairloom.utils), [1] L list (hairloom.datatypes.Segments attribute), [1] (hairloom.datatypes.Transitions attribute), [1] (hairloom.Segments attribute) (hairloom.Transitions attribute) M make_brk_table() (in module hairloom) (in module hairloom.utils), [1] make_bundle() (in module hairloom) (in module hairloom.collect), [1] make_seg_table() (in module hairloom) (in module hairloom.utils), [1] make_split_read_table() (in module hairloom.utils), [1] make_tra_table() (in module hairloom) (in module hairloom.utils), [1] make_tumor_sv_table() (in module hairloom.collect), [1] map_similar_coordinate_to_higher_rank() (in module hairloom.collect), [1] match (hairloom.datatypes.SplitAlignment attribute), [1] module hairloom hairloom.collect, [1] hairloom.datatypes, [1] hairloom.utils, [1] N normalize_sv_table() (in module hairloom) (in module hairloom.collect), [1] O ori (hairloom.Breakpoint attribute) (hairloom.datatypes.Breakpoint attribute), [1] P pclip1 (hairloom.datatypes.SplitAlignment attribute), [1] pos (hairloom.Breakpoint attribute) (hairloom.datatypes.Breakpoint attribute), [1] primary (hairloom.datatypes.SplitAlignment attribute), [1] pull_breakpoints_from_reads_in_sv_regions() (in module hairloom.collect), [1] pull_sv_supporting_reads_from_bundle() (in module hairloom.collect), [1] R read_name (hairloom.datatypes.SplitAlignment attribute), [1] refname (hairloom.datatypes.SplitAlignment attribute), [1] reverse_complement() (in module hairloom.utils), [1] S Segments (class in hairloom) (class in hairloom.datatypes), [1] segs (hairloom.BreakpointChain attribute) (hairloom.datatypes.BreakpointChain attribute), [1] seq_rearranged (hairloom.Breakpoint attribute) (hairloom.datatypes.Breakpoint attribute), [1] seq_removed (hairloom.Breakpoint attribute) (hairloom.datatypes.Breakpoint attribute), [1] SplitAlignment (class in hairloom.datatypes), [1] start (hairloom.datatypes.SplitAlignment attribute), [1] strand (hairloom.datatypes.SplitAlignment attribute), [1] T Transitions (class in hairloom) (class in hairloom.datatypes), [1] tras (hairloom.BreakpointChain attribute) (hairloom.datatypes.BreakpointChain attribute), [1] U upstream (hairloom.Breakpoint attribute) (hairloom.datatypes.Breakpoint attribute), [1]