I'm not sure if it's the case here, but I've noticed the CIGAR string has major issues if you attempt to include gaps in the clipped sequence.
Or rather CIGAR works fine I assume, but samtools does not. (It's not really a big issue as the only time I've seen this happen is someone manually trimming an alignment back.)
Or rather CIGAR works fine I assume, but samtools does not. (It's not really a big issue as the only time I've seen this happen is someone manually trimming an alignment back.)
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