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MaciekAber / pysam

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Samfile.fetch() does not return unmapped reads #18

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
What steps will reproduce the problem?
1. samfile.fetch() in a file with unmapped reads

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

Only mapped reads.

Please use labels and text to provide additional information.

as a patch use the option until_eof()
The problem: fetch() iterates only over target sequences,
but not over unmapped reads. Investigate file pos resetting.

Original issue reported on code.google.com by andreas....@gmail.com on 24 Oct 2009 at 1:54

GoogleCodeExporter commented 8 years ago

Original comment by andreas....@gmail.com on 4 May 2010 at 9:23