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Eric Banks ffaf92f871 Added new functionality to the FastaAlternateReferenceMaker to have it output IUPAC codes for het sites. 
Enable it with the new --useIUPAC argument.
Added both unit and integration tests for the new functionality - and fixed up the
exising tests once I was in there.
 		2014-03-12 14:31:57 -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
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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 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 Rename existing PipelineTests to QueueTests to prepare for upcoming push of new pipeline tests 2014-03-10 21:24:03 -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 Rename existing PipelineTests to QueueTests to prepare for upcoming push of new pipeline tests 2014-03-10 21:24:03 -04:00
repo Replaced local drmaa and Jama artifacts with versions from maven central. 2014-02-22 01:21:35 +08:00
sting-root Merge pull request #553 from broadinstitute/dr_rename_pipeline_tests 2014-03-10 21:36:45 -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