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Incompatibility with samtools version 1.3 #1

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pveber opened this issue May 10, 2017 · 1 comment
Open

Incompatibility with samtools version 1.3 #1

pveber opened this issue May 10, 2017 · 1 comment

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@pveber
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pveber commented May 10, 2017

If I'm not mistaken, the scritpt run_ataqc.py is broken due to a change of API in samtools sort, notably lines 522 and 524.

See samtools 1.3 release:

The obsolete samtools sort in.bam out.prefix usage has been removed. If you are still using ‑f, ‑o, or out.prefix, convert to use -T PREFIX and/or -o FILE instead.

Could be nice to document this version constraint or would you be accepting a patch to update the script?
@vervacity
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Hi,

Thanks for the heads up. We'll do both - document for now, and if any patches come our way we're happy to accept! :)

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@pveber @vervacity