carneiro 5e9a8f9cb3 Implemented a new argument (-DQS --defaultQualityScore) that allows GATK to deal with BAM files missing quality scores. If a value is specified, all reads are filled with the default quality score. Appropriate exception is thrown if -DQS is not provided and BAM file doesn't have quality scores for every base. ... Adding the first version of the techdev pipeline (tdPipeline) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4943 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-05 22:25:08 +00:00
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BoundedReadIteratorUnitTest.java	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00
LocusIteratorByStateUnitTest.java	Implemented a new argument (-DQS --defaultQualityScore) that allows GATK to deal with BAM files missing quality scores. If a value is specified, all reads are filled with the default quality score. Appropriate exception is thrown if -DQS is not provided and BAM file doesn't have quality scores for every base.	2011-01-05 22:25:08 +00:00
StingSAMIteratorAdapterUnitTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00