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Valentin Ruano-Rubio 98ffcf6833 Get gVCF to work without --dontTrimActiveRegions 
Story:

https://www.pivotaltracker.com/story/show/65048706
https://www.pivotaltracker.com/story/show/65116908

Changes:

ActiveRegionTrimmer in now an argument collection and it returns not only the trimmed down active region but also the non-variant containing flanking regions
HaplotypeCaller code has been simplified significantly pushing some functionality two other classes like ActiveRegion and AssemblyResultSet.

Fixed a problem with the way the trimming was done causing some gVCF non-variant records no have conservative 0,0,0 PLs
 		2014-02-05 22:50:45 -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 Bumped version to 2.8-SNAPSHOT, using new update_pom_versions.sh script. 2014-02-03 13:50:46 -05:00
gatk-framework Get gVCF to work without --dontTrimActiveRegions 2014-02-05 22:50:45 -05:00
gatk-package Bumped version to 2.8-SNAPSHOT, using new update_pom_versions.sh script. 2014-02-03 13:50:46 -05:00
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 Bumped version to 2.8-SNAPSHOT, using new update_pom_versions.sh script. 2014-02-03 13:50:46 -05:00
java/config Moved files to maven directories. 2014-02-03 13:50:44 -05:00
package-tests Distinct failsafe summary reports, just like invoker report directories. 2014-02-03 13:50:47 -05:00
perl Fixing the liftover script to not require strict VCF header validation. 2013-11-07 09:02:17 -05:00
queue-framework Bumped version to 2.8-SNAPSHOT, using new update_pom_versions.sh script. 2014-02-03 13:50:46 -05:00
queue-package Bumped version to 2.8-SNAPSHOT, using new update_pom_versions.sh script. 2014-02-03 13:50:46 -05:00
repo Switched commited dependency repository from ivy to maven. 2014-02-03 13:50:46 -05:00
sting-root Bumped version to 2.8-SNAPSHOT, using new update_pom_versions.sh script. 2014-02-03 13:50:46 -05:00
sting-utils Bumped version to 2.8-SNAPSHOT, using new update_pom_versions.sh script. 2014-02-03 13:50:46 -05:00
pom.xml Bumped version to 2.8-SNAPSHOT, using new update_pom_versions.sh script. 2014-02-03 13:50:46 -05:00