AddCommentsToBam function does not handle colon in the -C flag
open | Created 2018-10-16 | Last updated 2018-10-17| Posted by esamorodnitsky | See in Github


Barclay bug


Bug Report

Affected tool(s) or class(es)

AddCommentsToBam

Affected version(s)

  • Latest public release version [version?] GATK-4.0.10.1

Description

I was trying to run AddCommentsToBam and with the -C flag, it was crashing when I had a colon in the string, so I had to delete it.

Steps to reproduce

gatk AddCommentsToBam -I=In.bam -O=Out.bam -C="Bad: comment"
gatk AddCommentsToBam -I=In.bam -O=Out.bam -C="Good comment"

Expected behavior

A new BAM with the comment should be created.

Actual behavior

I get this output: No value found for tagged argument: C=Bad: comment


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