gatk-3.8/public/java/test/org/broadinstitute/sting
Mark DePristo ff26f2bf68 HierarchicalMicroScheduler no longer attempts to wrap exceptions
-- This behavior, which isn't obviously valuable at all, continued to grab and rethrow exceptions in the HMS that, if run without NT, would show up as more meaningful errors.  Now HMS simply checks whether the throwable it received on error was a RuntimeException.  If so, it is stored and rethrow without wrapping later.  If it isn't, only in this case is the exception wrapped in a ReviewedStingException.
-- Added a QC walker ErrorThrowingWalker that will throw a UserException, ReviewedStingException, and NullPointerException from map as specified on the command line
-- Added IT that ensures that all three types are thrown properly (i.e., you catch a NullPointerException when you ask for one to be thrown) with and without threading enabled.
-- I believe this will finally put to rest all of these annoying HMS captures.
2012-03-23 11:27:21 -04:00
..
alignment Reinitialize random seed in the bwa bindings from the fixed seed stored in the 2011-07-22 13:41:53 -04:00
commandline Added ability to specify arguments in files via -args/--arg_file 2011-10-24 15:58:34 -04:00
gatk HierarchicalMicroScheduler no longer attempts to wrap exceptions 2012-03-23 11:27:21 -04:00
jna When using bam list mode in HSP deriving VCF name from bam list instead of requiring an additional parameter. 2011-12-16 18:09:25 -05:00
utils Add a conversion from the deprecated PL ordering to the new one. We need this for the DiploidSNPGenotypeLikelihoods which still use the old ordering. My intention is for this to be a temporary patch, but changing the ordering in DiploidSNPGenotypeLikelihoods is not appriopriate for committing to stable as it will break all of the external tools (e.g. MuTec) that are built on top of the class. We will have to talk to e.g. Kristian to see how disruptive this will be. Added unit tests to the GL conversions and indexing. 2012-03-16 11:14:37 -04:00
BaseTest.java CalibrateGenotypeLikelihoods now emits the position of the variant for debugging 2012-03-09 16:00:07 -05:00
MD5DB.java Merged bug fix from Stable into Unstable 2011-10-13 18:02:06 -04:00
MedianUnitTest.java Adding more unit tests and contracts to PairHMM util class. Updating HaplotypeCaller to use the new PairHMM util class. Now that the HMM result isn't dependent on the length of the haplotype there is no reason to ensure all haplotypes have the save length which simplifies the code considerably. 2012-03-05 08:28:42 -05:00
StingTextReporter.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
WalkerTest.java Minor: cleaner way of turning off index-on-the-fly checking in case we want to turn it back on. 2012-03-18 00:53:29 -04:00