Phillip Dexheimer b348ce8f25 Added -disableOptimizations argument to HaplotypeCaller. ... * This argument is intended to be used in conjunction with -bamout, and disable early-exit optimizations to allow reference regions to be contained in the output bam * Also forcibly includes the reference haplotype in the set of haplotypes given to the BAMWriter * Made -dontTrimActiveRegions visible, as it is likely also desirable in this use case * Addresses PT 77731660		2014-10-16 21:11:20 -04:00
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src	Added -disableOptimizations argument to HaplotypeCaller.	2014-10-16 21:11:20 -04:00
pom.xml	Now passing in the path to the GATK directory to tests.	2014-09-02 01:40:59 +08:00