Re: [Samtools-help] samtools sort problem

[John M. <jm...@sa...>]

On 10 Oct 2016, at 05:35, Juan Daniel Montenegro Cabrera <jdm...@gm...> 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  Having identified the outdated code, this will be easy to fix.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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