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brittneybrinsfield / pysam

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Add AlignedRead.addTags for speed improvement #146

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
I have a function converting a sam to abam file , adding a read group tag to 
all reads.

I was able to shave of about 20% of the runtime by adding an explicit addTag 
function - savings are mostly by not decoding and recoding the existing tags, 
but copying their bytes verbatim.

See patch, including test cases, for implementation.

Original issue reported on code.google.com by finkerna...@mathematik.uni-marburg.de on 13 Dec 2013 at 9:48

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GoogleCodeExporter commented 9 years ago 
Thanks, great stuff!

Will add as soon as I can.

Best wishes,
Andreas

Original comment by andreas....@gmail.com on 17 Dec 2013 at 10:10

GoogleCodeExporter commented 9 years ago 
The patch has been added, many thanks!

May I add you to the author list in AUTHORS?

Best wishes,
Andreas

Original comment by andreas....@gmail.com on 20 Dec 2013 at 9:23

GoogleCodeExporter commented 9 years ago 
>May I add you to the author list in AUTHORS?

Sure :). Thank you.

Original comment by f.finker...@googlemail.com on 3 Jan 2014 at 8:01

GoogleCodeExporter commented 9 years ago 
Added.

Original comment by andreas....@gmail.com on 19 Feb 2014 at 9:50