On 31 Oct 2014, at 12:38, Nick Loman <n.j.lo...@bham.ac.uk> wrote:
> Latest build of samtools (1.1) mpileup core dumps with the following file
> (produced with latest BWA and samtools on nanopore data) in -g (BCF) or -v
> (VCF) mode, e.g..
>
> samtools mpileup -Q 0 -f NC_000913.fna -g Ecoli_R73_2D.bam
[...]
> http://pathogenomics.bham.ac.uk/filedist/nanopore/Ecoli_R73_2D.bam
>
> Any ideas anyone?
Some quality time spent with the debugger :-) shows that the problem here is
that BAQ recalculation (in bam_prob_realn_core()) is corrupting some of your
reads in memory, which then leads to crashes when the later RG lookup tries to
parse that read's auxiliary data. I haven't finished figuring out what's going
on here, but there is certainly a bug for us to fix -- perhaps exhibited
because your reads don't have base qualities.
In the meantime, a possible workaround is to disable BAQ recalculation with
mpileup -B.
Thanks for the test data and bug report.
John
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