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gatk3的最后一个经典版本3.8
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Scala 3.8%
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Mark DePristo 0d593cff70 Refactor rsID and overlap detection in VariantOverlapAnnotator utility class 
-- Variants will be considered matching if they have the same reference allele and at least 1 common alternative allele.  This matching algorithm determines how rsID are added back into the VariantContext we want to annotate, and as well determining the overlap FLAG attribute field.
-- Updated VariantAnnotator and VariantsToVCF to use this class, removing its old stale implementation
-- Added unit tests for this VariantOverlapAnnotator class
-- Removed GATKVCFUtils.rsIDOfFirstRealVariant as this is now better to use VariantOverlapAnnotator
-- Now requires strict allele matching, without any option to just use site annotation.
 		2013-06-10 15:51:13 -04:00
licensing Removing the symlink from the private license file 2013-02-09 12:57:44 -05:00
protected Refactor rsID and overlap detection in VariantOverlapAnnotator utility class 2013-06-10 15:51:13 -04:00
public Refactor rsID and overlap detection in VariantOverlapAnnotator utility class 2013-06-10 15:51:13 -04:00
settings Rev picard, sam-jdk, tribble, and variant to version 1.91.1453 2013-05-07 14:21:15 -04:00
.gitignore Detect stuck lock-acquisition calls, and disable file locking for tests 2013-04-24 22:49:02 -04:00
build.xml Restore scala compilation by default in build.xml 2013-05-31 11:28:29 -04:00
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