gatk3的最后一个经典版本3.8

Eric Banks 05e69b6294 Refactoring of SlidingWindow class in RR to reduce complexity and fix important bug. ... * Allow RR to write its BAM to stdout by setting required=true for @Output. * Fixed bug in sliding window where a break in coverage after a long stretch without a variant region was causing a doubling of all the reads before the break. * Refactored SlidingWindow.updateHeaderCounts() into 3 separate tested methods. * Refactored polyploid consensus code out of SlidingWindow.compressVariantRegion().		2013-03-12 09:06:55 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Refactoring of SlidingWindow class in RR to reduce complexity and fix important bug.	2013-03-12 09:06:55 -04:00
public	Two features useful for ancient DNA processing.	2013-03-09 18:18:13 -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	Fix tests that were consistently or intermittently failing when run in parallel on the farm	2013-03-06 13:56:54 -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	Brought all of ReduceReads to fastutils	2013-02-23 22:53:23 -05:00