Parser of CIGAR strings.
Parser of CIGAR strings.
(->placeholder cigar-str)
Creates an encoded placeholder from a given CIGAR string. The placeholder is in the format of kSmN where k is the read length and m is the reference length. Returns a vector of ints.
Creates an encoded placeholder from a given CIGAR string. The placeholder is in the format of kSmN where k is the read length and m is the reference length. Returns a vector of ints.
(count-op s)
Returns length of CIGAR operations.
Returns length of CIGAR operations.
Returns length of reference bases.
Returns length of reference bases.
(count-ref-bytes cigar-bytes)
Count covering length in reference from encoded CIGAR byte-array.
Count covering length in reference from encoded CIGAR byte-array.
(decode-cigar-and-ref-length cigar-bytes)
Decode CIGAR string and length of alignment in reference. Returns a vector of [cigar, ref-length].
Decode CIGAR string and length of alignment in reference. Returns a vector of [cigar, ref-length].
(encode-cigar cigar)
Encodes CIGAR string into a sequence of longs.
Encodes CIGAR string into a sequence of longs.
(parse s)
Parses CIGAR string, returning a sequence of lengths and operations.
Parses CIGAR string, returning a sequence of lengths and operations.
(placeholder? cigar-bytes)
Returns a boolean indicating whether a CIGAR is in kSmN
format.
Returns a boolean indicating whether a CIGAR is in `kSmN` format.
(simplify cigs)
Merge contiguous same operations of parsed CIGAR.
Merge contiguous same operations of parsed CIGAR.
(to-index* s)
Convert CIGAR string to sequence of indices.
Convert CIGAR string to sequence of indices.
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