On Tue, Aug 02, 2016 at 11:57:52AM +0200, Martin MOKREJ? wrote:
> Could samtools calmd apply the following logic for bwa-processed input?
> Get positions of all N's in the read.
> Do not complain about those positions which are based on N's.
> Do report other positions.
I don't entirely understand what you're wanting.
Calmd computes the MD:Z tag as described in the SAM specification,
which is difference between the sequence and the reference. It should
not be changed to some other algorithm, no matter what aligners happen
to do. If aligners produce different MD tags then they are buggy.
Similarly for NM:i.
> OK, I know "samtools calmd" reports a total sum of the differences before and
> after but quite likely there will be only a "0 -> 0" to be reported. So I
> will get less warning on the screen, which is always good. ;)
The warnings are there because it is correcting the aligner output.
The proper fix is to fix the aligners to produce the correct MD in the
first place, not to break calmd to be buggy in the same manner.
James
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