gatk3的最后一个经典版本3.8

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Eric Banks a3d55b3341 Make sure to fail in all cases where the BAM being used was created by ReduceReads. In some cases, the program records were being removed from the BAM headers by the GATK engine before we applied the check for reduced reads (so we did not fail appropriately). Pushed up the check to happen before the PG tags are modified and added a unit test to ensure it stays that way. It turns out that some UG tests still used reduced bams so I switched to use different ones. Based on reviewer feedback, made it more generic so that it's easy to add new unsupported tools.		2014-04-03 16:52:41 -04:00
licensing	deleted old license files	2013-07-02 16:36:47 -04:00
protected	Make sure to fail in all cases where the BAM being used was created by ReduceReads.	2014-04-03 16:52:41 -04:00
public	Make sure to fail in all cases where the BAM being used was created by ReduceReads.	2014-04-03 16:52:41 -04:00
settings/helpTemplates	Replaced local drmaa and Jama artifacts with versions from maven central.	2014-02-22 01:21:35 +08:00
.gitignore	Fixed bug using GraphBased due to infinite likelihoods resulting from the calculation of alignment cost of very long insertion or deletions (done in linear scale)	2014-04-01 16:14:52 -04:00
README.md	Update README file for the 2.6 release	2013-06-20 13:08:29 -04:00
ant-bridge.sh	Rename existing PipelineTests to QueueTests to prepare for upcoming push of new pipeline tests	2014-03-10 21:24:03 -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
pom.xml	Update pom versions to mark the start of GATK 3.2 development	2014-03-18 01:18:59 -04:00

README.md

The Genome Analysis Toolkit

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