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Joel Thibault 2049eb1658 Rev Picard 1.110.1763 
- SamPairUtils migrated in Picard r1737
- Revert IndelRealigner changes made in commit 4f4b85
-- Those changes were based on Picard revision 1722 to net/sf/picard/sam/SamPairUtil.java
-- Picard revision 1723 reverts these changes, so we also revert to match
 		2014-03-30 09:33:57 -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 3.2 development 2014-03-18 01:18:59 -04:00
gatk-framework Fix for dropping of reference sample depth in the DP annotation. 2014-03-24 14:01:50 -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 Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00
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 1.110.1763 2014-03-30 09:33:57 -04:00
sting-root Rev Picard 1.110.1763 2014-03-30 09:33:57 -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