samtools calmd -r

[a11msp]

Dear colleagues,

I'm trying out samtools in the new calmd -r mode (compute base alignment quality) and since it's a very recent feature and not yet fully documented, just wanted to check whether it has done what it's supposed to do.

I've run it as follows:

samtools calmd -br s2_bwa.bam genome.fa > s2_bwa_calmd.bam

After about an hour with ~30 M reads, the run finished and the output file was created.

The output to stderr was something like this:

[bam_fillmd1] different NM for read 'HWI-EAS225_0029_FC:5:25:3128:3739#0': 0 -> 2
[bam_fillmd1] different MD for read 'HWI-EAS225_0029_FC:5:25:3128:3739#0': '76' -> '0N0N74'
[bam_fillmd1] different NM for read 'HWI-EAS225_0029_FC:5:33:8287:16578#0': 0 -> 1
[bam_fillmd1] different MD for read 'HWI-EAS225_0029_FC:5:33:8287:16578#0': '76' -> '0N75'
....
....

I'm just wondering whether this output reflects only the 'old' part of the calmd function and the new one didn't produce output - or I'm actually misunderstanding what exactly the BAQ function does to the data (I understand, in very general terms, what it does from the algorithmic point of view, but not sure I got the technical side).

Many thanks!