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)
Counts covering length in reference from encoded CIGAR byte-array.
Counts covering length in reference from encoded CIGAR byte-array.
(decode-cigar-and-ref-length cigar-bytes)
Decodes CIGAR string and length of alignment in reference. Returns a vector of [cigar, ref-length].
Decodes 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)
Merges contiguous same operations of parsed CIGAR.
Merges contiguous same operations of parsed CIGAR.
Converts from CIGAR string to sequence of indices. This function is memoized.
Converts from CIGAR string to sequence of indices. This function is memoized.
(to-index* s)
Converts CIGAR string to sequence of indices.
Converts CIGAR string to sequence of indices.
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