bwa-mem2 cannot recognize the input from the pipe about bwa-meth

[brentp]

Thanks. I have pushed that change and tagged v0.2.4

[brentp]

does it work with /dev/stdin instead of - ?

[yewero]

It works well with /dev/stdin:

bwameth.py c2t t_R1.fastq.gz t_R2.fastq.gz | \
bwa-mem2 mem -T 40 -B 2 -L 10 -CM -U 100 -p -R '@RG\tID:t_R\tSM:t_R' -t 12  ref.fa.bwameth.c2t /dev/stdin

[brentp]

@PoisonAlien , should we make the change to /dev/stdin ?

[PoisonAlien]

Yes, I am ok with the change. I have been using this tool for a while now and, it's weird that I have never encountered it earlier. Regardless, this is probably the robust way than a dash since it is universally available.