Eric Banks 3759d9dd67 Added the functionality to impose a relative ordering on ReadTransformers in the GATK engine. ... * ReadTransformers can say they must be first, must be last, or don't care. * By default, none of the existing ones care about ordering except BQSR (must be first). * This addresses a bug reported on the forum where BAQ is incorrectly applied before BQSR. * The engine now orders the read transformers up front before applying iterators. * The engine checks for enabled RTs that are not compatible (e.g. both must be first) and blows up (gracefully). * Added unit tests.		2013-03-06 12:38:59 -05:00
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sting	Added the functionality to impose a relative ordering on ReadTransformers in the GATK engine.	2013-03-06 12:38:59 -05:00