Guillermo del Angel 963ad03f8b Second step of interface cleanup for variant annotator: several bug fixes, don't hash pileup elements to Maps because the hashCode() for a pileup element is not implemented and strange things can happen. Still several things to do, not done yet		2012-08-19 21:18:18 -04:00
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src/org/broadinstitute/sting	Second step of interface cleanup for variant annotator: several bug fixes, don't hash pileup elements to Maps because the hashCode() for a pileup element is not implemented and strange things can happen. Still several things to do, not done yet	2012-08-19 21:18:18 -04:00
test/org/broadinstitute/sting/gatk/walkers	Fix for performance problem in GGA mode related to previous --regenotype commit. Instead of trying to hack around the determination of the calculation model when it's not needed, just simply overload the calculateGenotypes() method to add one that does simple genotyping. Re-enabling the Pool Caller integration tests.	2012-08-16 13:05:17 -04:00