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Valentin Ruano-Rubio c167fb5fdf Fixing GenotypesGVCF. 
Bug uncovered by some untrimmed alleles in the single sample pipeline output.

Notice however does not fix the untrimmed alleles in general.

Story:

https://www.pivotaltracker.com/story/show/65481104

Changes:

1. Fixed the bug itself.
2. Fixed non-working tests (sliently skipped due to exception in dataProvider).
 		2014-02-19 14:20:39 -05:00
..
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 Fixed build bug in ./ant-bridge.sh unittest -Dsingle=..., due to external-example. 2014-02-15 13:52:20 +08:00
gatk-framework Fixing GenotypesGVCF. 2014-02-19 14:20:39 -05:00
gatk-package Create symlinks target/GenomeAnalysisTK.jar and target/Queue.jar during package phase. 2014-02-15 01:12:32 +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 Exclude all transitive dependencies in maven package-tests 2014-02-12 14:59:05 -05:00
perl Fixing the liftover script to not require strict VCF header validation. 2013-11-07 09:02:17 -05:00
queue-framework Add ability to run *KnowledgeBaseTests to maven 2014-02-11 14:08:24 -05:00
queue-package Create symlinks target/GenomeAnalysisTK.jar and target/Queue.jar during package phase. 2014-02-15 01:12:32 +08:00
repo Rev Picard to 1.107.1683 (4 jars) 2014-02-12 15:25:50 -05:00
sting-root Fixed build bug in ./ant-bridge.sh unittest -Dsingle=..., due to external-example. 2014-02-15 13:52:20 +08:00
sting-utils 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
pom.xml Adding the external example to the build. 2014-02-15 01:26:07 +08:00