CG tag and SEQ/CIGAR consistency. - #2089
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BAM has this check at the end, but SAM checks after reading SEQ and before checking if we'll overwrite CIGAR with a CG tag. CRAM uses bam_set1, which checks for SEQ/CIGAR consistency, but this is also prior to aux tag parsing and CG->CIGAR migration. The nature of the bam_set1 API though is such that aux tags haven't yet been parsed, so it is up to the caller to perform this test itself later or to parse aux and replace cigar before calling bam_set1. CRAM does however call bam_tag2cigar as even though it doesn't need it, it's there for consistency of what takes priority. sam_parse1 calls that function too, and potentially third party code, so checking has been added there as well. Credit to OSS_Fuzz Fixes oss-fuzz issue 560967311 Signed-off-by: James Bonfield <jkb@sanger.ac.uk>
Normally this is detected and filtered out earlier, but see the previous commit. So we take the belt and braces approach and fix it here too. Signed-off-by: James Bonfield <jkb@sanger.ac.uk>
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BAM moves the CG: cigar tag to the CIGAR field prior to validating sequence length and the cigar fields are logically consistent.
SAM does the consistency check before parsing CG, so it could fail. CRAM likewise. (Although technically both formats do not need to parse the tag, they do so for consistency with BAM.)