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brittneybrinsfield / pysam

Automatically exported from code.google.com/p/pysam
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output BAM does not have EOF marker #78

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1.outfile.write(), outfile.close()
2.
3.

What is the expected output? What do you see instead?
The outfile should be a complete BAM file but when I tried samtools view 
outfile, it complained that EOF marker is missing.

What version of the product are you using? On what operating system?
Pysam 0.5 on UNIX

Please provide any additional information below.

Original issue reported on code.google.com by yanc...@gmail.com on 26 Oct 2011 at 8:38

GoogleCodeExporter commented 9 years ago 
Thanks.

Your example seems incomplete. How did you open outfile?

Best wishes,
Andreas

Original comment by andreas....@gmail.com on 27 Oct 2011 at 7:28

GoogleCodeExporter commented 9 years ago 
This may be due to a bug in samtools itself when anything other than the 
default compression level is used. See samtools mailing list and 
https://github.com/lh3/samtools/pull/7

Original comment by p.j.a.c...@googlemail.com on 2 Feb 2012 at 4:46

GoogleCodeExporter commented 9 years ago 
Thanks, I will close this issue for now.

Please re-open if this continues to be a problem.

Best wishes,
Andreas

Original comment by andreas....@gmail.com on 10 Jul 2012 at 9:13