Color Space mate-pairs generated by AB SOLiD machines orient FF or RR in Maq, because that is how they are sequenced from the original molecule: "same orientation, same direction."
The result of this when using Maq on CS mate-pair reads is that they are incorrectly treated and discarded under many circumstances. For example, in 'maq assemble' the -p option will discard ALL correctly oriented mate-paired reads, and only retain a tiny minority of incorrectly oriented reads. Maq assemble probably needs a -c option to inform it that SOLiD pairing rules should apply.
Other Maq commands and documentation (e.g. mapview, pileup, indelpe and indelsoa) are almost certainly also affected and need to be informed that SOLiD data is being processed.
Vaughn
vsi [at] u.washington.edu
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Thank you for the bug reporting. I will postpone this fix, as I am releasing maq-0.6.8 and do not want to add new bugs when fixing old. I will keep this ticket open until I fix it.
Cheers,
Heng