gatk3的最后一个经典版本3.8

Geraldine Van der Auwera 61349ecefa Cleaned up annotations ... - Moved AverageAltAlleleLength, MappingQualityZeroFraction and TechnologyComposition to Private - VariantType, TransmissionDisequilibriumTest, MVLikelihoodRatio and GCContent are no longer Experimental - AlleleBalanceBySample, HardyWeinberg and HomopolymerRun are Experimental and available to users with a big bold caveat message - Refactored getMeanAltAlleleLength() out of AverageAltAlleleLength into GATKVariantContextUtils in order to make QualByDepth independent of where AverageAltAlleleLength lives - Unrelated change, bundled in for convenience: made HC argument includeUnmappedreads @Hidden - Removed unnecessary check in AverageAltAlleleLength		2013-03-14 14:26:48 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Cleaned up annotations	2013-03-14 14:26:48 -04:00
public	Cleaned up annotations	2013-03-14 14:26:48 -04:00
settings	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
.gitignore	Fixing the licensing scripts	2013-01-26 13:42:49 -05:00
build.xml	Fix tests that were consistently or intermittently failing when run in parallel on the farm	2013-03-06 13:56:54 -05:00
intellij_example.tar.bz2	Removed the intellij files from the root and made an example package for new users. This allows users to start at the same page and then change it as they see fit without interfering with the repo (thanks guillermo!)	2012-09-27 11:04:56 -04:00
ivy.xml	Brought all of ReduceReads to fastutils	2013-02-23 22:53:23 -05:00