gatk3的最后一个经典版本3.8

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Eric Banks fa65716fe9 Added code to retrieve dangling heads from the read threading graph (previously we were rescuing just the tails). The purpose of this is to be able to call SNPs that fall at the beginning of a capture region (or exon). Before, the read threading code would only start threading from the first kmer that matched the reference. But that means that, in the case of a SNP at the beginning of an exome, it wouldn't start threading the read until after the SNP position - so we'd lose the SNP. For now, this is still very experimental. It works well for RNAseq data, but does introduce FPs in normal exomes. I know why this is and how to fix it, but it requires a much larger fix to the HC: the HC needs to pass all reads and bases to the annotation engine (like UG does) instead of just the high quality ones. So for now, the head merging is disabled by default. As per reviewer comments, I moved the head and tail merging code out into their own class.		2014-03-03 15:59:26 -05:00
licensing	deleted old license files	2013-07-02 16:36:47 -04:00
protected	Added code to retrieve dangling heads from the read threading graph (previously we were rescuing just the tails).	2014-03-03 15:59:26 -05:00
public	Moving Reduce Reads to the archive.	2014-03-02 02:03:14 -05:00
settings/helpTemplates	Replaced local drmaa and Jama artifacts with versions from maven central.	2014-02-22 01:21:35 +08:00
.gitignore	Adding the external example to the build.	2014-02-15 01:26:07 +08:00
README.md	Update README file for the 2.6 release	2013-06-20 13:08:29 -04:00
ant-bridge.sh	Add ability to run *KnowledgeBaseTests to maven	2014-02-11 14:08:24 -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
pom.xml	Separate failsafe directories for each of the integration test types [#66515572 ]	2014-02-27 04:43:39 +08:00

README.md

The Genome Analysis Toolkit

See http://www.broadinstitute.org/gatk/