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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