David Roazen 932cd3ada7 Fix 3rd-party library dependency issues in the HC/PairHMM tests ... In general, test classes cannot use 3rd-party libraries that are not also dependencies of the GATK proper without causing problems when, at release time, we test that the GATK jar has been packaged correctly with all required dependencies. If a test class needs to use a 3rd-party library that is not a GATK dependency, write wrapper methods in the GATK utils/* classes, and invoke those wrapper methods from the test class.		2013-12-06 13:16:55 -05:00
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R	Something changed with the ggtitle syntax in the latest version of ggplot2.	2013-08-14 14:40:03 -04:00
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	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
java	Fix 3rd-party library dependency issues in the HC/PairHMM tests	2013-12-06 13:16:55 -05:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	ValidatingPileup was renamed to CheckPileup	2013-02-15 11:56:19 -05:00
perl	Fixing the liftover script to not require strict VCF header validation.	2013-11-07 09:02:17 -05:00
scala	New VCF engine arguments to specify an alternate IndexCreator	2013-12-03 13:31:02 -05:00
testdata	Walker to create a fastq file from an interval list	2013-06-29 11:24:16 -04:00