gatk3的最后一个经典版本3.8

Mauricio Carneiro 8ae2e7be4f Queue scripts to process call and assess callsets (for AGBT13) ... a quick data-processing pipeline: -- only adding basic steps from aligned bam to recalibrated bam. -- paired down from the multitude of options of the data processing pipeline -- one bam in, one bam out -- Implemented the "fly" mode to the quick processing pipeline -- because "quick" wasn't quick enough... calling and assess pipeline: -- takes in a list of bams -- calls using both UG and HC with and without BQSR -- can optionally skip bqsr if recalibration report is not provided (assumes bam already is recalibrated) GSATDG-76 GSATDG-75 GSATDG-58 GSATDG-57 GSATDG-56 GSATDG-52 GSATDG-51		2013-02-22 10:19:01 -05:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected/java	Bug fix in LikelihoodCalculationEngine: Mapping quality was being cast to a byte and overflowing for reads with large mapping quality scores.	2013-02-21 14:34:17 -05:00
public	Relax bounds checking in QualityUtils.boundQual	2013-02-22 08:46:59 -05:00
settings	Haplotype/Allele based optimizations for the HaplotypeCaller that knock off nearly 20% of the total runtime (multi-sample).	2013-02-21 10:14:11 -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