make bwa-mem output reproducible upon changing number of threads
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pmenzel commented
According to lh3/bwa#121, the bwa-mem output is not stable upon changing the number of threads.
Maybe it would be good to set -K 10000000 as suggested by lh3 to make the results reproducible here:
https://github.com/jodyphelan/TBProfiler/blob/57d54be5069aa2c34c463d4576a55240dab17f9f/pathogenprofiler/fastq.py#L61
Not sure if it also affects bwa-mem2.
jodyphelan commented
Hi @pmenzel,
Thanks for letting me know, I'll put this in.