found two problems: * i was reusing the fastq var within the file which could lead to issues * i was also looping through all read groups a second time when it   wasn't needed leading to files being checked multiple times.
found two problems:
* i was reusing the fastq var within the file which could lead to issues
* i was also looping through all read groups a second time when it
  wasn't needed leading to files being checked multiple times.

statgen/csg-utils,statgen/csg-utils,statgen/csg-utils