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David Roazen 1324120c17 Unconditionally include all of commons-httpclient in the GATK/Queue jars 
The maven shade plugin was eliminating a necessary class (IgnoreCookiesSpec)
when packaging the GATK/Queue. Work around this by telling maven to
always package all of commons-httpclient.
 		2014-03-14 10:50:15 -04:00
..
VectorPairHMM Removed g_haplotype* global variables in native code so that it works 2014-03-06 22:08:35 -08:00
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
external-example Update pom versions to mark the start of GATK 3.1 development 2014-03-06 00:05:58 -05:00
gatk-framework Added new functionality to the FastaAlternateReferenceMaker to have it output IUPAC codes for het sites. 2014-03-12 14:31:57 -04:00
gatk-package Unconditionally include all of commons-httpclient in the GATK/Queue jars 2014-03-14 10:50:15 -04:00
gatk-queue-extgen Update pom versions to mark the start of GATK 3.1 development 2014-03-06 00:05:58 -05:00
gsalib Update pom versions to mark the start of GATK 3.1 development 2014-03-06 00:05:58 -05:00
java/config Moved files to maven directories. 2014-02-03 13:50:44 -05:00
package-tests Rename existing PipelineTests to QueueTests to prepare for upcoming push of new pipeline tests 2014-03-10 21:24:03 -04:00
perl Fixing the liftover script to not require strict VCF header validation. 2013-11-07 09:02:17 -05:00
queue-framework Rename existing PipelineTests to QueueTests to prepare for upcoming push of new pipeline tests 2014-03-10 21:24:03 -04:00
queue-package Unconditionally include all of commons-httpclient in the GATK/Queue jars 2014-03-14 10:50:15 -04:00
repo Replaced local drmaa and Jama artifacts with versions from maven central. 2014-02-22 01:21:35 +08:00
sting-root Unconditionally include all of commons-httpclient in the GATK/Queue jars 2014-03-14 10:50:15 -04:00
sting-utils Merge remote-tracking branch 'origin/master' into intel 2014-03-10 14:07:36 -04:00
pom.xml Rename existing PipelineTests to QueueTests to prepare for upcoming push of new pipeline tests 2014-03-10 21:24:03 -04:00