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Old 09-04-2012, 01:55 AM   #1
mccullocha
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Location: New Zealand

Join Date: Apr 2011
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Default how to check integrity/completeness of bwa sai files ?

We would like to check the integrity/completeness of sai file
output from bwa -aln, to ensure that this output has not been
silently truncated by either disk quota exceeded or other i/o glitches.
Ideally we would like to parse the sai file and verify that
all input sequences appear in the sai output - either with a
valid suffix array index, or a null entry.

Is this possible using either one of the bwa commandline options,
or alternatively parsing the file with a custom script
(Or some other way) ? How is it best done ?
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