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andyrimmer / Platypus

Platypus Variant Caller
GNU General Public License v3.0
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Platypus input from .csi indexed BAMs #86

Closed MaximilianStammnitz closed 4 years ago

MaximilianStammnitz commented 4 years ago

Hi Andy,

My permissions to write in the Platypus user group are still pending, so hope it’s okay if I’d directly write in here for now.

I am trying to call variants on a genome with (a few) very large chromosomes, hence mappings against this can only be indexed through CSI rather than BAI. When trying to input such an alignment, placed in the same folder as the corresponding CSI, Platypus throws the following error.

Wondering if there’s a quick fix to this by also allowing Platypus to find CSI files instead?

Many thanks, Max

MaximilianStammnitz commented 4 years ago

[Okay, that was a rather simple fix - can be solved by installing the latest htslib (1.10)]