Yep, it was the latter, thanks for noticing!
On Mon, Aug 15, 2016 at 1:06 PM, Thomas W. Blackwell <tbla...@umich.edu>
wrote:
>
> 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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