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Khalid Shakir a894a2dddb Updates to GATK classes and POMs that need updating, plus RodSystemValidation md5 updates. 
GATK classes accessing package protected htsjdk classes changed to new package names.
POMs updated to support merging of sam/tribble/variant -> htsjdk and changes to picard artifact.
RodSystemValidation outputs changed due to variant codec packages changes, requiring test md5 updates.
Second of four commits for picard/htsjdk package rename.
 		2014-05-08 19:13:27 +08:00
..
VectorPairHMM Removed scary warning messages for VectorPairHMM 2014-05-06 10:59:24 -07:00
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 Updates to GATK classes and POMs that need updating, plus RodSystemValidation md5 updates. 2014-05-08 19:13:27 +08:00
gatk-framework Updates to GATK classes and POMs that need updating, plus RodSystemValidation md5 updates. 2014-05-08 19:13:27 +08:00
gatk-package Updates to GATK classes and POMs that need updating, plus RodSystemValidation md5 updates. 2014-05-08 19:13:27 +08:00
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 Updates to GATK classes and POMs that need updating, plus RodSystemValidation md5 updates. 2014-05-08 19:13:27 +08:00
repo Rev Picard 1.111.1920 2014-04-16 14:39:19 -04:00
sting-root Updates to GATK classes and POMs that need updating, plus RodSystemValidation md5 updates. 2014-05-08 19:13:27 +08:00
sting-utils Updates to GATK classes and POMs that need updating, plus RodSystemValidation md5 updates. 2014-05-08 19:13:27 +08:00
pom.xml Update pom versions to mark the start of GATK 3.2 development 2014-03-18 01:18:59 -04:00