gatk3的最后一个经典版本3.8

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Eric Banks 6bee6a1b53 Change the behavior of SelectVariants for PL/AD when it encounters a record that has lost one or more alternate alleles. Previously, we would strip out the PLs and AD values since they were no longer accurate. However, this is not ideal because then that information is just lost and 1) users complain on the forum and post it as a bug and 2) it gives us problems in both the current and future (single sample) calling pipelines because we subset samples/alleles all the time and lose info. Now the PLs and AD get correctly selected down. While I was in there I also refactored some related code in subsetDiploidAlleles(). There were no real changes there - I just broke it out into smaller chunks as per our best practices. Added unit tests and updated integration tests. Addressed reviews.		2013-12-03 09:23:03 -05:00
licensing	deleted old license files	2013-07-02 16:36:47 -04:00
protected	Change the behavior of SelectVariants for PL/AD when it encounters a record that has lost one or more alternate alleles.	2013-12-03 09:23:03 -05:00
public	Change the behavior of SelectVariants for PL/AD when it encounters a record that has lost one or more alternate alleles.	2013-12-03 09:23:03 -05:00
settings	Tweaked gatkdocs index template	2013-11-19 15:05:41 -05:00
.gitignore	Detect stuck lock-acquisition calls, and disable file locking for tests	2013-04-24 22:49:02 -04:00
README.md	Update README file for the 2.6 release	2013-06-20 13:08:29 -04:00
build.xml	Resolving warnings	2013-09-23 12:42:22 -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	Changing from scala 2.9.2 to 2.10.2.	2013-09-23 12:42:22 -04:00

README.md

The Genome Analysis Toolkit

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