Disabling pipefail when the output is explicitely troncated

arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery

MIT License

309 stars 118 forks source link

Disabling pipefail when the output is explicitely troncated #230

Open vdanjean opened 6 years ago

vdanjean commented 6 years ago

"grep -m 1" stop after the first found occurence. "samtools view" stop with an error if its output is closed. With pipefail, the samtools error is taken into account by the lumpyexpress script that immediately exits

The error do not always occurs: if the information looked after by grep is at the end of the BAM file and samtools is able to complete before its output is closed, then no error occurs But we have several BAM files that triggered this error.

vdanjean commented 6 years ago

The travis-ci error does not seem to be due to my patch...