On Tue, Aug 02, 2016 at 01:44:01PM +0200, Martin MOKREJ? wrote:
> >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.
>
> Hmm, but bwa mem did not introduce the MD: tag, see the lines from
>
> samtools view mysample-PB.bam | grep HWI-xxxxx:xxx:xxxxxxxxx:2:1101:1110:65038
>
> in a previous email.
Ok fair enough, consider my maligning of the aligner rescinded!
However the point is still valid; somewhere some tool wrote incorrect
MD tags. It is not appropriate to make Samtools gloss over these
errors, or worse, change the algorithm to compute things in the same
broken manner.
It may be worth studying the @PG lines to figure out where the duff MD
tags came from and send in a bug report.
> So, I still think "samtools calmd" could be less verbose.
It's a valid warning, but maybe there should be a silent mode.
However with non-broken data you'll find it is very quiet so
collectively I think the effort should be placed at fixing the
tool that produced data. :-)
James
--
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| Plurima gyrabant gymbolitare vabo;
A Staden Package developer: | Et Borogovorum mimzebant undique formae,
https://sf.net/projects/staden/ | Momiferique omnes exgrabure Rathi.
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