Does not allow DS field in PG record

[GoogleCodeExporter]

When reading the header of a bam file with a DS fields in a PG record a 
ValueError is thrown:

In [1]: import pysam

In [2]: s = pysam.Samfile('file.bam')

In [3]: s.header
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-3-694a9732a0b6> in <module>()
----> 1 s.header

/Users/val/anaconda/lib/python2.7/site-packages/pysam/csamtools.so in 
pysam.csamtools.Samfile.header.__get__ (pysam/csamtools.c:16139)()

ValueError: unknown field code 'DS' in record 'PG'

It turns out "DS" is not listed under "PG" in VALID_HEADER_FIELDS in the file 
csamtools.pyx, this is inconsistent with the SAM spec: 
http://samtools.sourceforge.net/SAMv1.pdf

The problem is fixed by modifying line 367 of pysam/csamtools.pyx from

                        "PG" : { "PN" : str, "ID" : str, "VN" : str, "CL" : str, "PP" : str}, 

to

                        "PG" : { "PN" : str, "ID" : str, "VN" : str, "CL" : str, "PP" : str , "DS" : str}, 

Original issue reported on code.google.com by valentin...@gmail.com on 22 Jan 2014 at 10:39

[GoogleCodeExporter]

Hi Valentine,

many thanks for reporting this, fixed.

Best wishes,
Andreas

Original comment by andreas....@gmail.com on 19 Feb 2014 at 9:34

• Changed state: Fixed