Add sort options - Githubissues

bcgsc / tigmint

⛓ Correct misassemblies using linked AND long reads

https://bcgsc.github.io/tigmint/

GNU General Public License v3.0

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Add sort options #73

Closed PuneetSS closed 2 years ago

PuneetSS commented 2 years ago

Added sort option parameter to samtools sort and sort
Updated README

mmokrejs commented 2 years ago

But this could also be pushed to arcs and probably LINKS source trees as well, right? Why not making the behavior consistent across all your tools?

mmokrejs commented 2 years ago

And, more importantly, the SORT_OPTS should not be propagated to both sort and samtools sort commandlines but only to the former. samtools sort -S 10G yields an error. Did you test this, @PuneetSS ?

lcoombe commented 2 years ago

Thank you for pointing out that the command options should only be added to sort, not samtools sort - @PuneetSS will open a fresh PR making that fix.

I'm not sure that we have a sort command (other than samtools sort, which as you pointed out shouldn't pass these options) in ARCS or LINKS, but definitely feel free to open a PR in either repo if you had an idea for a different command.