ASCII quality scores in BAM output

[ben berman]

We have been running BS-MAP directly with Illumina input files ("-z @"
mode), which contain Illumina quality score ASCII codes (Phred+64).
The BAMs that come out still have the Illumina quality values, but
unfortunately this is invalid BAM. The BAM spec (http://
samtools.sourceforge.net/SAM1.pdf) specifically states that quality
scores must be in Sanger format (Phred+33). So the BAM's produced by
BSMAP are not legal for publishing, and will not work correctly with
many downstream processing tools. The solution should be pretty
simple, just subtract 31 from the quality scores if "-z @" mode is
being used.

Does this make sense?

ben.