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nilesh-iiita / pysam

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NotImplementedError: tags field too large #100

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1.Read in the only read in the bam file as an AlignedRead object.
2.Attempt to create a new AlignedRead object containing XA tag attributes of 
the original AlignedRead object.
3.

What is the expected output? What do you see instead?
NotImplementedError is raised because size of XA tag (string) attached to new 
AlignedRead object is too large.

What version of the product are you using? On what operating system?
pysam 0.6, samtools 0.1.18, tabix 0.2.5, linux 64bit 96GB RAM.

Please provide any additional information below.

ERROR:
oread.tags = tuple(tags)
  File "csamtools.pyx", line 2363, in csamtools.AlignedRead.tags.__set__ (pysam/csamtools.c:20660)
NotImplementedError: tags field too large

Original issue reported on code.google.com by drhpa...@gmail.com on 8 Oct 2012 at 1:22

Attachments:

GoogleCodeExporter commented 9 years ago 
Fixed. The limit on the field length was arbitrary and has been removed.

Best wishes,
Andreas

Original comment by andreas....@gmail.com on 8 Oct 2012 at 2:44