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jpelletier888 / ea-utils

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mapped bases didn't output #9

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. launch sam-stats -B bamfile > stat_file

What is the expected output? What do you see instead?
I expect to have the mapped base as describe in help "mapped bases      : total 
of the lengths of the aligned reads" 
But it isn't.

What version of the product are you using? On what operating system?
svn version 1.31

Original issue reported on code.google.com by noirot.c...@gmail.com on 29 May 2012 at 3:48

GoogleCodeExporter commented 9 years ago 
Can you post an example file?   Preferably the smallest one you can make?

Original comment by earone...@gmail.com on 29 May 2012 at 3:57

GoogleCodeExporter commented 9 years ago 
here it is a little one

Original comment by noirot.c...@gmail.com on 30 May 2012 at 1:52

Attachments:

GoogleCodeExporter commented 9 years ago 
ok, new ver (373) outputs "tmapb" under the label "mapped bases"  .. you can 
also dervice this number by multiplying the mean length by the mapped reads.

Original comment by earone...@gmail.com on 31 May 2012 at 1:41

GoogleCodeExporter commented 9 years ago

Original comment by earone...@gmail.com on 31 May 2012 at 1:41