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Chris Whelan e61ba8b340 Added command line checks for duplicate files in ROD lists 
-- Keep a list of processed files in ArgumentTypeDescriptor.getRodBindingsCollection
  -- Throw user exception if a file name duplicates one that was previously parsed
  -- Throw user exception if the ROD list is empty
  -- Added two unit tests to RodBindingCollectionUnitTest
 		2014-02-27 13:32:18 -05:00
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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
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doc Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs) 2013-03-12 10:57:14 -04:00
external-example Fixed mvn run for packagetests over external-example. 2014-02-22 01:21:34 +08:00
gatk-framework Added command line checks for duplicate files in ROD lists 2014-02-27 13:32:18 -05:00
gatk-package Fixed scope for test-jar depedencies. 2014-02-22 01:21:34 +08:00
gatk-queue-extgen Bumped version to 2.8-SNAPSHOT, using new update_pom_versions.sh script. 2014-02-03 13:50:46 -05:00
gsalib Added a set of serial tests to gatk/queue packages, which runs all tests under their package in one TestNG execution. 2014-02-06 08:25:38 -05:00
java/config Moved files to maven directories. 2014-02-03 13:50:44 -05:00
package-tests Separate failsafe directories for each of the integration test types [#66515572] 2014-02-27 04:43:39 +08:00
perl Fixing the liftover script to not require strict VCF header validation. 2013-11-07 09:02:17 -05:00
queue-framework Added tests for cleaning up scattered .bai files, and using the log directory. 2014-02-26 02:11:28 +08:00
queue-package Fixed scope for test-jar depedencies. 2014-02-22 01:21:34 +08:00
repo Replaced local drmaa and Jama artifacts with versions from maven central. 2014-02-22 01:21:35 +08:00
sting-root Separate failsafe directories for each of the integration test types [#66515572] 2014-02-27 04:43:39 +08:00
sting-utils Replaced local drmaa and Jama artifacts with versions from maven central. 2014-02-22 01:21:35 +08:00
pom.xml Adding the external example to the build. 2014-02-15 01:26:07 +08:00