Hi,
Sometimes we get reads to align that have been trimmed to zero length and
I'm wondering how these should be represented in SAM format.
Here's a pair as reported by Novoalign that had been trimmed by cutadapt
and one read of the pair is zero length
READID 77 * 0 0 * * 0 0 * PG:Z:novoalign
READID 141 * 0 0 * * 0 0
GTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAGGGG
EEDDB:=<;A9/=C=@A;:<,1:<?@.0<./;;;AC.;;5@:: PG:Z:novoalign
The first read of the pair has a zero length SEQ field.
This pair fails with a parse error in Samtools Version: 1.2 (using htslib
1.2.1) but is accepted by Samtools Version: 0.1.19-44428cd.
What is a valid SAM record for a zero length read?
Thanks, Colin
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