Ryan Poplin fe3069b278 Merged bug fix from Stable into Unstable		2012-08-22 14:40:34 -04:00
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bqsr	Re-enabling parallelism in the BaseRecalibrator now that the release is out.	2012-08-20 21:25:14 -04:00
compression/reducereads	Fixed divide by zero bug when downsampler goes over regions where reads are all filtered out. Added Guillermo's bug report as an integration test	2012-08-09 13:02:11 -04:00
genotyper	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
haplotypecaller	Merged bug fix from Stable into Unstable	2012-08-22 14:40:34 -04:00