Ryan Poplin 2e5f9db758 Raising per-sample limits on the number of reads in ART and HC. ... -- Active Region Traversal was using per sample limits on the number of reads that were too low, especially now that we are running one sample at a time. This caused issues with high confidence variants being dropped in high coverage data. -- HaplotypeCallerGVCFIntegrationTest PL/annotation changes due to using more reads in those tests -- Removed a CountReadsInActiveRegionsIntegrationTest test for excessive coverage because the read coverage no longer goes over the limits in ART		2015-01-09 11:21:42 -05:00
..
VectorPairHMM	Do not use logger, write to stderr, could not get the correct logger dependency in pom.xml	2015-01-06 10:32:11 -05:00
c	After renaming the packages, instead of updating the JNI library used for testing bwa, moving the classes to the archive.	2014-05-19 17:36:41 -04:00
chainFiles	The contig is named MT not M in b36. Delivers PT68890442.	2014-04-08 10:03:47 -04:00
doc	Refactored maven directories and java packages replacing "sting" with "gatk".	2014-05-19 17:36:39 -04:00
external-example	Faster builds, with updates to documentation generation.	2014-11-05 00:32:23 +08:00
gatk-engine	Raising per-sample limits on the number of reads in ART and HC.	2015-01-09 11:21:42 -05:00
gatk-queue	Faster builds, with updates to documentation generation.	2014-11-05 00:32:23 +08:00
gatk-queue-extensions-generator	Split all imports of tools|engine from utils, and all tools from engine.	2014-10-24 20:59:46 +08:00
gatk-queue-extensions-public	Adding Axiom_Exome_Plus.sites_only.all_populations.poly.vcf to the resource bundle because it is used in the v3.3 best practices	2015-01-05 14:52:31 -05:00
gatk-root	Merge pull request #768 from broadinstitute/pd_bcf_failures	2014-10-31 15:30:56 -04:00
gatk-tools-public	Fix mmultiallelic info field annotation for VariantAnnotator	2014-12-17 22:21:00 -05:00
gatk-utils	Merge pull request #792 from broadinstitute/rhl_pairhmm_log_stderr	2015-01-07 12:41:10 -05:00
gsalib	Updated gsalib version to 2.1 for resubmitting with updated license to CRAN	2014-12-09 17:07:48 -05:00
java/config	Refactored maven directories and java packages replacing "sting" with "gatk".	2014-05-19 17:36:39 -04:00
package-tests	Split all imports of tools|engine from utils, and all tools from engine.	2014-10-24 20:59:46 +08:00
perl	Fixing the liftover script to not require strict VCF header validation.	2013-11-07 09:02:17 -05:00
repo	Revved Picard/htsjdk	2014-10-30 21:16:25 -04:00
src/main	Added faster built executable, non-packaged jars.	2014-11-05 00:30:46 +08:00
pom.xml	Update pom versions to mark the start of GATK 3.4 development	2014-10-23 22:31:44 -04:00