Eric Banks 562f2406d7 Added check that BaseRecalibrator is not being run on a reduced bam. ... - Throws user exception if it is. - Can be turned off with --allow_bqsr_on_reduced_bams_despite_repeated_warnings argument. - Added test to check this is working. - Added docs to BQSRReadTransformer explaining why this check is not performed on PrintReads end. - Added small bug fix to GenomeAnalysisEngine that I uncovered in this process. - Added comment about not changing the program record name, as per reviewer comments. - Removed unused variable.		2013-02-06 10:14:27 -05:00
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java	Added check that BaseRecalibrator is not being run on a reduced bam.	2013-02-06 10:14:27 -05:00