Multiple 'PG' lines not supported

[GoogleCodeExporter]

What steps will reproduce the problem?
1. Use Picard to merge multiple BAM files together into one
2. Open the file and access the 'header' field in pysam

What is the expected output? What do you see instead?

Multiple PG lines should be supported.  There are many instances where a
"merged" BAM file is desired, and some SAM -> BAM converters do not merge
the @PG fields together.  The BAM file is still valid and works with
samtools and other programs.  Therefore pysam should handle this situation.

What version of the product are you using? On what operating system?

pysam-v1.1a hacked a bit to work with python 2.5.

Thanks for providing this great tool to the community,

Best,
Matthew

Original issue reported on code.google.com by matthew....@gmail.com on 7 Dec 2009 at 1:55

[GoogleCodeExporter]

Original comment by andreas....@gmail.com on 4 May 2010 at 9:25

[GoogleCodeExporter]

Original comment by andreas....@gmail.com on 4 May 2010 at 9:46

• Changed state: Accepted

[GoogleCodeExporter]

Thanks, it should work now [PG files will treated the same as RG fields].

Fixed for version 0.2

Original comment by andreas....@gmail.com on 4 May 2010 at 10:01

• Changed state: Fixed