SAMTools appears to read tags with negative values incorrectly. If I create the following sample file:
@SQ SN:seq1 LN:1000
B7_591:4:96:693:509 73 seq1 1 99 36M * 0 0 CACTAGTGGCTCATTGTAAATGTGTGGTTTAACTCG <<<<<<<<<<<<<<<;<<<<<<<<<5<<<<<;:<;7 XA:i:-120
and use the command
samtools view -S test.sam
the output is
B7_591:4:96:693:509 73 seq1 1 99 36M * 0 0 CACTAGTGGCTC
ATTGTAAATGTGTGGTTTAACTCG <<<<<<<<<<<<<<<;<<<<<<<<<5<<<<<;:<;7 XA:i:136
The value of the tag XA is displayed as 136 instead of -120. Is this a bug or am I doing something incorrectly?
Thanks!
@SQ SN:seq1 LN:1000
B7_591:4:96:693:509 73 seq1 1 99 36M * 0 0 CACTAGTGGCTCATTGTAAATGTGTGGTTTAACTCG <<<<<<<<<<<<<<<;<<<<<<<<<5<<<<<;:<;7 XA:i:-120
and use the command
samtools view -S test.sam
the output is
B7_591:4:96:693:509 73 seq1 1 99 36M * 0 0 CACTAGTGGCTC
ATTGTAAATGTGTGGTTTAACTCG <<<<<<<<<<<<<<<;<<<<<<<<<5<<<<<;:<;7 XA:i:136
The value of the tag XA is displayed as 136 instead of -120. Is this a bug or am I doing something incorrectly?
Thanks!
Comment