Crate intspan

Structs

• Coverage
• FasBlock
  A Fas alignment block.
• FasEntry
• IntSpan
  IntSpan handles of sets containing integer spans.
• LinesRef
• MafBlock
  A MAF alignment block.
• MafEntry
  An alignment entry within a MAF block. Corresponds to the “s” line.
• Overlap
• Range
• Substitution

Functions

• absolute_path
• align_seqs
  Returns Strings to avoid lifetime issues
• align_seqs_quick
• align_to_chr
  Coordinate transforming - from align to chr
• alignment_stat
  Basic stats on alignments
• basename
• build_range_of_part
• chr_to_align
  Coordinate transforming - from chr to align
• chrs_in_sets
• fill_up_m
• fill_up_s
• get_consensus_poa
• get_seq_faidx
• get_subs
  Returns unpolarized substitutions
• indel_intspan
• json2set
• json2set_m
• next_axt_block
  Get the next Axt block out of the input.
• next_fas_block
  Get the next FasBlock out of the input.
• next_maf_block
  Get the next MafBlock out of the input.
• pair_d
  Divergence (D) between two sequences
• parse_axt_block
• parse_fas_block
• parse_maf_block
• polarize_subs
  Polarize substitutions
• read_first_column
• read_json
• read_lines
• read_replaces
• read_sizes
• reader
• seq_intspan
• set2json
• set2json_m
• sort_links
• trim_complex_indel
  Records complex ingroup indels (ingroup-outgroup complex indels are not identified here)
• trim_head_tail
  Trims head and tail indels. Returns a Vecter of Tuple(head, tail) corresponding to the bases deleted from each sequence
• trim_outgroup
  Trims outgroup-only regions
• trim_pure_dash
  Trims pure dash regions
• write_json
• write_lines
• writer