Hello,
I observe a strange problem and I am not able to find out what is the exact
reason of it. When I use "samtools mpileup | another_program", samtools
return error code 141. Everything else is OK (pileup is well created, all
data are well processed). I observe it when I use "set -o pipefail". The
overall return error status is 141 and it is really caused by samtools
because
echo "${PIPESTATUS[0]} ${PIPESTATUS[1]}"
141 0
It is interesting that this problem appears only with pipes. When I save
the output of samtools to a file, the error code is 0.
Do you have any ideas about the reason?
Thanks
Karel
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