Utility functions for SAM optional fields.
Utility functions for SAM optional fields.
(alternative-hits aln)
List of alternative alignments.
List of alternative alignments.
(edit-distance aln)
Edit distance from reference of the alignment.
Edit distance from reference of the alignment.
(mate-cigar aln)
CIGAR string of the mate alignment.
CIGAR string of the mate alignment.
(mismatching-positions aln)
Mismatching positions and bases of the alignment.
Mismatching positions and bases of the alignment.
(parse-alternative-hits-str s)
Parse serialized supplementary alignments.
Parse serialized supplementary alignments.
(parse-mismatching-positions-str s)
Parse mismatching positions in the SAM optional fields. Returns a sequence consisting of vectors which are one of [:match matching-length], [:mismatch a-reference-base-char] and [:deletion reference-bases-string].
Parse mismatching positions in the SAM optional fields. Returns a sequence consisting of vectors which are one of [:match matching-length], [:mismatch a-reference-base-char] and [:deletion reference-bases-string].
(parse-supplementary-alignments-str s)
Parse serialized supplementary alignments.
Parse serialized supplementary alignments.
(primary-to-alt-score aln)
Ratio of the primary alignment score and the alternative one.
Ratio of the primary alignment score and the alternative one.
(read-group aln)
Name of read group of the alignment.
Name of read group of the alignment.
(ref-comment aln)
Comment of reference sequence.
Comment of reference sequence.
(suboptimal-score aln)
Suboptimal alignment score.
Suboptimal alignment score.
(supplementary-alignments aln)
List of supplementary alignments.
List of supplementary alignments.
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