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cljam.io.sam.util.cigar

Parser of CIGAR strings.

Parser of CIGAR strings.
raw docstring

count-opclj

(count-op s)

Returns length of CIGAR operations.

Returns length of CIGAR operations.
sourceraw docstring

count-refcljmultimethod

Returns length of reference bases.

Returns length of reference bases.
sourceraw docstring

count-ref-bytesclj

(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.
sourceraw docstring

decode-cigar-and-ref-lengthclj

(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].
sourceraw docstring

encode-cigarclj

(encode-cigar cigar)

Encodes CIGAR string into a sequence of longs.

Encodes CIGAR string into a sequence of longs.
sourceraw docstring

parseclj

(parse s)

Parses CIGAR string, returning a sequence of lengths and operations.

Parses CIGAR string, returning a sequence of lengths and operations.
sourceraw docstring

simplifyclj

(simplify cigs)

Merge contiguous same operations of parsed CIGAR.

Merge contiguous same operations of parsed CIGAR.
sourceraw docstring

to-indexclj

source

to-index*clj

(to-index* s)

Convert CIGAR string to sequence of indices.

Convert CIGAR string to sequence of indices.
sourceraw docstring

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