gatk3的最后一个经典版本3.8

Mark DePristo 35139cf990 HaplotypeScore only annotates SNPs ... -- The new HMM new edge conditions the likelihoods are offset by log10(n possible starts) so the results don't really mean "fits the haplotype well" any longer. This results in grossly inflated HaplotypeScores for indels and with the HaplotypeCaller. So I'm simply not going to emit this annotation value any longer for indels and for the HC		2013-02-09 19:19:28 -05:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected/java	HaplotypeScore only annotates SNPs	2013-02-09 19:19:28 -05:00
public	Final version of PairHMMs with correct edge conditions	2013-02-09 19:19:22 -05:00
settings	Replace org.broadinstitute.variant with jar built from the Picard repo	2013-02-05 17:24:25 -05:00
.gitignore	Fixing the licensing scripts	2013-01-26 13:42:49 -05:00
build.xml	Minor build.xml cleanup post-variant-migration	2013-02-06 11:16:52 -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	Replace org.broadinstitute.variant with jar built from the Picard repo	2013-02-05 17:24:25 -05:00