David Roazen 639030bd6d Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements ... -Diff engine output is now included in the actual exception message thrown as a result of an MD5 mismatch, which allows it to be conveniently viewed on the main page of a build in Bamboo. Minor Additional Improvements: -WalkerTestSpec now auto-detects test class name via new JVMUtils.getCallingClass() method, and the test class name is now included as a regular part of integration test output for each test. -Fix race condition in MD5DB.ensureMd5DbDirectory() -integrationtests dir is now cleaned by "ant clean" GSA-915 #resolve		2013-05-10 19:00:33 -04:00
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R	Improve queue script jobreport visualization script	2013-05-07 12:11:46 -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	Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements	2013-05-10 19:00:33 -04:00
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	Split out contig names from Reference .fai file on white space (to support the GATK resource bundle's file human_g1k_v37.fasta.fai.gz, which does not use tab delimiters)	2012-06-07 16:56:32 -04:00
scala	Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements	2013-05-10 19:00:33 -04:00
testdata	Revert changes to exampleFASTA.fasta.fai for now to get tests passing again	2013-05-02 12:59:20 -04:00