gatk3的最后一个经典版本3.8

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Valentin Ruano-Rubio 3cdeab6e9e GenotypingEngines and walkers now use AFCalc(ulator) providers rathern than instanciate their own (fixed) calculators directly. Changes: ------- * GenotypingEngine uses now a AFCalc provider instead of its own thread-local with one-time initialized and fixed AF calculator. * All walkers that use a GenotypingEngine now are passing the appropiate AF calculator provider. For now most just use a fix calculator (FixedAFCalculatorProvider) except GenotypeGVCFs as this one now can cope with mixture of ploidies failing-over to a general-ploidy calculator when the preferred implementation is not capable to handle a site's analysis.		2014-09-12 14:25:09 -04:00
licensing	deleted old license files	2013-07-02 16:36:47 -04:00
protected	GenotypingEngines and walkers now use AFCalc(ulator) providers rathern than instanciate their own (fixed) calculators directly.	2014-09-12 14:25:09 -04:00
public	GenotypingEngines and walkers now use AFCalc(ulator) providers rathern than instanciate their own (fixed) calculators directly.	2014-09-12 14:25:09 -04:00
settings/helpTemplates	changed the GATKDocs format to PHP	2014-08-18 18:04:07 -04:00
.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	Refactored maven directories and java packages replacing "sting" with "gatk".	2014-05-19 17:36:39 -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	Now passing in the path to the GATK directory to tests.	2014-09-02 01:40:59 +08:00

README.md

The Genome Analysis Toolkit

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