Are you using 'samtools sort' or just 'sort' which resolves to '/usr/bin/sort'
?
(This sorting behavior sounds like the latter.)
- tom blackwell -
On Mon, 15 Aug 2016, David Siegel wrote:
> Greetings
>
> I've installed Samtools successfully on my Mac (downloaded the file,
> unpacked it, cd'd into the folder, typed "make" on the command line, tested
> it on a SAM file, and it worked fine). The command I'm using is: sort -n
> --output testfile_sorted_aligned ~/Documents/blahblahAligned.out.sam
>
> I also installed it onto my work cluster (a unix-based environment), and it
> worked ok but had a weird bug: It sorted the header file alphabetically in
> addition to the mapped SAM data. So some of the header data now comes at
> the end of the file, some of it comes at the beginning.
>
> If this is really the only issue I can always just write code to get around
> it. But if it's a common symptom of some sort of error in installation,
> could someone let me know how to fix it?
>
> I'm also not the most savvy individual when it comes to the unix/linux
> environment, I've only been using it for a few months.
>
> Thanks,
>
> David
>
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