bamtools resolve removes quality string?

[ekg]

I have some simulated reads which I've aligned with Mosaik, then sorted. At a certain point I realized that the reason that samtools wasn't calling anything from the data was that it only works on proper pairs, so I added bamtools resolve into my pipeline. The result seems to make GATK unhappy sometimes. It notes that there are no quality bases attached to a particular read.

This is what happens to the read. Before:

% bamtools merge -in sample06.bam | samtools view - | grep sample06.000003491
# first mate
sample06.000003491      145     chr20_bit       2124    65      1S69M   =       1796    -396    GTTTGATGGGTGAGTGCACTGTAACTTCCAGACGTCTCTTGGTAGGTGGGCCCCACTGGCCAAGGGCATT  *AIIICFII>IIGDIHIIIIIEIDIIIIDEIHGGIEHEFIIIIDGHHIIEIHIGIIHHGIHHHIHIHHHH    RG:Z:sample06   NM:i:0  MD:Z:69 ZA:Z:<&;63;0;;1;70M;70><@;61;0;;1;;>
% bamtools resolve -twoPass -in sample06.bam | samtools view - | grep sample06.000003491
# first mate unaffected
sample06.000003491      147     chr20_bit       2124    65      1S69M   =       1796    -396    GTTTGATGGGTGAGTGCACTGTAACTTCCAGACGTCTCTTGGTAGGTGGGCCCCACTGGCCAAGGGCATT  *       RG:Z:sample06     NM:i:0  MD:Z:69 ZA:Z:<&;63;0;;1;70M;70><@;61;0;;1;;>

I can deliver a full test case off-thread.

[pezmaster31]

Ah, I'll bet you anything the bug is with the leading '*' character in the quality string, getting interpreted a la SAM ('missing'). I'll take a look at it this weekend. Thanks for the heads-up.

[ekg]

That looks like the problem. I think I can work around it for now. Glad
you've already been informed.

On Fri, Dec 7, 2012 at 11:15 PM, Derek Barnett notifications@github.comwrote:

Ah, I'll bet you anything the bug is with the leading '*' character in the
quality string, getting interpreted a la SAM ('missing'). I'll take a look
at it this weekend. Thanks for the heads-up.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/68#issuecomment-11148761.

[ekg]

If the fix in my repository doesn't have unintended side-effects, it should be sufficient to resolve this problem.