Closed eboyden closed 1 year ago
I believe that SNAP has the property that you describe.
I'd have to do some due diligence to make sure that there aren't any other differences between SAM v 1.4 and 1.6 that we'd need to observe, however.
This is in 2.0.2.dev.9. Let me know if it does what you want.
In 2.0.2
Unless I'm mistaken, paired-end alignments (without the
-so
option) inevitably produce unsorted but query-grouped outputs. Several downstream tools such asfgbio
include functions that insist on name-sorted or query-grouped inputs, and rely on the@HD
line to confirm this. Without theGO:query
tag present, either it needs to be added manually, or the file needs to be unnecessarily (re)-collated just to add this tag.