On 10 Oct 2016, at 05:35, Juan Daniel Montenegro Cabrera
<jdmonteneg...@gmail.com> wrote:
> I did a few test in my spare time. All samtools version from 0.1.19 have the
> same sorting problem, with or without the use of (-@) multiple threads.
> Version 0.1.18 is able to sort the file correctly, but is slower than
> sambamba, especially for really big bam files.
> I have a reduce unsorted bam file of ~500Mb that can be used to reproduce
> this issue.
Thanks for the sample file. Looking at the properly-sorted and badly-sorted
6B_concat reads, it turns out that the wrongly-processed ones are those that
have positions greater than 2^30.
The problem is some code in samtools sort that was written back when
chromosomes were limited to 2^29 bases, and that doesn't work for positions
beyond 2^30. Having identified the outdated code, this will be easy to fix.
Thanks for the bug report.
John
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