[Bio-bwa-help] PG line issue

[Joel M. <j_m...@lb...>]

Hello,
  I'm starting to use the gatk and noticed this issue on their forums today
with bwa mem adding command line to the PG line and ending up with multiple
ID: key/value pairs

 @PG <http://gatkforums.broadinstitute.org/profile/PG> ID:bwa PN:bwa
VN:0.7.10-r789 CL:bwa mem -R @RG
<http://gatkforums.broadinstitute.org/profile/RG> ID:X LB:Y SM:Z
PL:ILLUMINA ref.fa R1_001_filtered.fastq R2_001_filtered.fastq; File
alignment.bam; Line number 43

it's not clear from the sam spec that the first ID:VAL should be used, it
just says it should be unique so I think this makes it illegal.  gatk
throws an error on it, would it make sense to put the command line in a
subsequent @CO line?

Joel