View Single Post
Old 01-16-2013, 01:46 AM   #11
priesgo
Member
 
Location: Spain

Join Date: Aug 2012
Posts: 22
Default

Hi,

I'm in the same situation as Bruce. I want to compress keeping the base call qualities but can't figure out how...

Just did a naf try:
Code:
--lossy-quality-score-spec all
and got:
Code:
Exception in thread "main" java.lang.RuntimeException: Uknown read or base category: a
        at net.sf.cram.lossy.QualityScorePreservation.parseSinglePolicy(QualityScorePreservation.java:138)
So apparently you can specify a read name to keep the quality, not of use in my case as I want to keep all of them; and base category. But, what is the base category? I also tried a numeric value in case it referred referred to an index in the read, but with similar result.


Thanks!
Pablo.
priesgo is offline   Reply With Quote