SAM format: negative values in tags

[viola1]

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!

[Simon Anders]

I'd say, it is a bug. According to the spec, 'i' means "Signed 32-bit integer".

Now, as 136 is the two's complement of 120 in 8-bit arithmetics, it seems that samtools somewhere converts to short ints.

Simon

[jmarshall]

This samtools bug was fixed in late November in subversion (change 514), but the current 0.1.7a release is from a little before then.

If this is causing difficulty, you might want to apply the (very simple) patch linked above yourself. The problem is only in using samtools to display the data; the correct negative value is stored in any generated BAM files, etc.

[viola1]

Thank you both for confirming this!