On 11 Feb 2015, at 13:12, Sendu Bala <s...@sanger.ac.uk> wrote:
> I'm using the latest samtools (1.1) and picard (1.128).
>
> If I make a bam using the -u option of eg. calmd, it now creates a raw
> uncompressed bam (as opposed to a bgzip bam with compression level 0, which
> is what samtools v0 did).
As Peter correctly surmised, this was an unintended change.
The effect of bgzf_open(fame, "wu") was changed on the road to version 1.0 [1]
for the sake of bcftools and being able to specify uncompressed VCF and raw BCF
and so on.
Unfortunately calmd -u also uses foo_open(fname, "wu") and suffered this change
in behaviour (since samtools version 1.0), when instead it should have been
updated to use foo_open(fname, "w0") to keep its existing behaviour.
The -u options of samtools merge, bamshuf, depad, and view are unaffected; they
use "w0" and still write compression-level-0 BAMs.
> Can compatibility be expected in the future, or should I develop a
> work-around?
In the next samtools release, we'll update samtools calmd -u to restore the
previous compatible behaviour. Apologies for the inconvenience.
John
[1]
https://github.com/samtools/htslib/commit/818a5ed171eb0cc3667a6c01845fca19a17d4478
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