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brentp / bwa-meth

fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
https://arxiv.org/abs/1401.1129
MIT License
141 stars 54 forks source link

add support for interleaved PE fastq #46

Closed bwlang closed 6 years ago

bwlang commented 6 years ago

It would be nice for bwameth to accept interleaved reads like bwa, so you can adapter trim on a pipe (like bwakit). Would you entertain a PR to that effect?

brentp commented 6 years ago

sure. should just be a boolean flag that matches the one in bwa mem (-p)