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Wrap minimap2 #128

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marvin-jens wants to merge 2 commits into main from wrap_minimap2

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marvin-jens commented Dec 2, 2024

Add functionality to integrate more mappers

especially minimap2.

extract FASTA/Q from uBAM
pipe it through whatever command
combine the output (SAM) with the original BAM tags
output complete SAM again

marvin-jens added 2 commits

November 18, 2024 11:48


          * add cmdline option to control total pipe_buffer usage. Limit to saf…

f5000f4

…e 4MB as long as we do not properly treat it as a resource


          * added plumbing to integrate aligners that need FASTA/Q as input and…

abdf733

… output SAM.

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