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Valentin Ruano-Rubio d563072282 Fix for CombineGVCFs and GenotypeGVCFs recurrent exception about missing PLs 
Story:

  https://www.pivotaltracker.com/story/show/68220438

Changes:

   - PL-less input genotypes are now uncalled and so non-variant sites when combining GVCFs.
   - HC GVCF/BP_RESOLUTION Mode now outputs non-variant sites in sites covered by deletions.
   - Fixed existing tests

Test:

   - HaplotypeCallerGVCFIntegrationTest
   - ReferenceConfidenceModelUnitTest
   - CombineGVCFsIntegrationTest
 		2014-05-02 09:21:06 -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 The contig is named MT not M in b36. Delivers PT68890442. 2014-04-08 10:03:47 -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 3.2 development 2014-03-18 01:18:59 -04:00
gatk-framework Fix for CombineGVCFs and GenotypeGVCFs recurrent exception about missing PLs 2014-05-02 09:21:06 -04:00
gatk-package Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00
gatk-queue-extgen Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00
gsalib Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00
java/config Moved files to maven directories. 2014-02-03 13:50:44 -05:00
package-tests Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00
perl Fixing the liftover script to not require strict VCF header validation. 2013-11-07 09:02:17 -05:00
queue-framework Removed setting of a default queue in PbsEngineJobRunner. Discussed here: http://gatkforums.broadinstitute.org/discussion/3959/would-it-be-possible-for-pbsengine-jobrunner-not-to-set-a-default-queue 2014-04-29 00:44:12 +08:00
queue-package Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00
repo Rev Picard 1.111.1920 2014-04-16 14:39:19 -04:00
sting-root Java 8 compatability fix: `Reflections` NPE bugfix. 2014-04-29 13:34:03 -04:00
sting-utils Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00
pom.xml Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00