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CRAM input support #27

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vinjana opened this issue Apr 21, 2021 · 0 comments
Open

CRAM input support #27

vinjana opened this issue Apr 21, 2021 · 0 comments

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@vinjana
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vinjana commented Apr 21, 2021 •
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Add support for CRAM files.

Note that biobambam2 uses io_lib, which relies on REF_PATH and REF_CACHE environment variables to specify the path to the reference file. See here. This means, probably these variables have to be used in conjunction with the inputformat=cram parameter (or cram3.1?)
@vinjana vinjana changed the title CRAM support CRAM input support Feb 23, 2024
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