It seems that this issue has come up a couple of times on the mailing listÖ

I think itís getting more relevant as people add more and more barcodes, fastq mapping is unappealing.

To solve my problem in the short term, Iím planning to explore
to rescue the read group information, but Iím not sure thatís going to work and I view it as a short-term workaround at best.

I prefer not to write hundreds of fastq files, before aligning reads.

Would a patch adding support for preserving read group information be accepted?

It looks like it will be a bit of work to implementÖ at least
- update the sai format to store the optional tags or build a tag set -> read data store
- modify samse and sampe to write tags back to sam

Any guidance would be appreciated.


Brad Langhorst, Ph.D.
Applications and Product Development Scientist