gatk-3.8/public
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
..
R Now converts gatkreports to properly typed R data types in gsa.read.gatkreport 2012-03-02 09:11:59 -05:00
c At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings. 2012-01-17 14:47:53 -05:00
chainFiles Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
doc Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
java HierarchicalMicroScheduler no longer attempts to wrap exceptions 2012-03-23 11:27:21 -04:00
keys Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -05:00
packages Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -05:00
perl Update to the bindings for liftOverVCF.pl (to -V from -B) 2011-09-15 15:33:09 -04:00
scala Mostly small changes to my own scala scripts: .vcf.gz compatibility for output files, smarter beagle generation, simple script to scatter-gather combine variants. Whole genome indel calling now uses the gold standard indel set. 2012-02-22 17:20:04 -05:00
testdata Added support for breakpoint alleles 2012-02-23 12:14:48 -05:00