Comments (3)
On second thought, it's (theoretically) possible to have both hard and soft clipping on the same end of the read. I don't know why you'd do that, but perhaps:
if ( (bam_cigar_opchr(c[i]) == 'S') || (bam_cigar_opchr(c[i]) == 'H'))
p += bam_cigar_oplen(c[i]);
should be
if ( (bam_cigar_opchr(c[i]) == 'S')
p += bam_cigar_oplen(c[i]);
else if ( bam_cigar_opchr(c[i]) != 'H')
break;
from seqlib.
Good catch. I agree that this is the right solution -- just pushed the commit.
from seqlib.
Thanks!
It looks like different flavors of the same bug are found elsewhere. Similar patches are needed at lines:
612
627
656
Thanks!
-August
from seqlib.
Related Issues (20)
- BamReader::SetCramReference HOT 3
- ChrName function in BamRecord Class logic wrong HOT 1
- minor bug found HOT 1
- Default Constructor may be optimized in case segment fault happens HOT 1
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- Looking for functionalities to replace BamTools with SeqLib
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from seqlib.