Guillermo del Angel 901f47d8af Final step (for now) in VA refactoring: update MD5's because, a) since it's not guaranteed that we'll iterate through reads/pileups in the same order, the rank sum dithering will change annotations, b) FS uses new generic threshold to distinguish uninformative reads (it used to use ad-hoc thresholds), c) AD definition changed and throws away uninformative reads, d) shortened general ploidy integration tests for quicker debugging. May have missed some MD5's in the update so there may be lingering test failures still		2012-08-22 11:38:51 -04:00
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src/org/broadinstitute/sting	Enable and adapt HaplotypeScore and MappingQualityZero as active region annotations now that we have per-read likelihoods passed in to annotations	2012-08-21 14:35:40 -04:00
test/org/broadinstitute/sting/gatk/walkers	Final step (for now) in VA refactoring: update MD5's because, a) since it's not guaranteed that we'll iterate through reads/pileups in the same order, the rank sum dithering will change annotations, b) FS uses new generic threshold to distinguish uninformative reads (it used to use ad-hoc thresholds), c) AD definition changed and throws away uninformative reads, d) shortened general ploidy integration tests for quicker debugging. May have missed some MD5's in the update so there may be lingering test failures still	2012-08-22 11:38:51 -04:00