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gatk-3.8/java/src/org/broadinstitute/sting
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depristo 8e129d76fd Support for original quality scores OQ flag. pQ flag in TableRecalibation to preserve quality scores below a threshold (defaulting to 5) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1474 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-08-28 14:14:21 +00:00
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gatk Support for original quality scores OQ flag. pQ flag in TableRecalibation to preserve quality scores below a threshold (defaulting to 5) 2009-08-28 14:14:21 +00:00
playground Removing min confidence for on/off genotype 2009-08-28 01:04:13 +00:00
secondarybase Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application. 2009-07-08 18:49:08 +00:00
utils Support for original quality scores OQ flag. pQ flag in TableRecalibation to preserve quality scores below a threshold (defaulting to 5) 2009-08-28 14:14:21 +00:00