cannot consume -.ubam on a pipe

Open bwlang opened this issue 5 years ago • 2 comments

samtools view ... | bam trimBam -.ubam -.ubam --clip -R

produces this error:

bam: invalid option -- '.'
ERROR: Unrecognized option left

works ok with

samtools view ...  |bam trimBam - - --clip -R

does work though

looks like a getopt problem to me.

May 29 '20 22:05 bwlang

You are correct, there was a getopt problem with that tool. I checked a fix into master. Please let me know if that resolves your problem. Thank you

Jun 02 '20 02:06 mktrost

seems to work for me now - thanks!

Jun 03 '20 16:06 bwlang