gatk3的最后一个经典版本3.8

David Roazen cdb1fa1105 Fix more tests that fail when run in parallel on the farm ... -Allow the default S3 put timeout of 30 seconds for GATKRunReports to be overridden via a constructor argument, and use a timeout of 300 seconds for tests. The timeout remains 30 seconds in all other cases. -Change integration tests that themselves dispatch farm jobs into pipeline tests. Necessary because some farm nodes are not set up as submit hosts. Pipeline tests are still run directly on gsa4. -Bump up the timeout for the MaxRuntimeIntegrationTest even more (was still occasionally failing on the farm!)		2013-03-12 16:53:30 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Use the indel heterozygosity prior when calling indels with the HC	2013-03-11 14:12:43 -04:00
public	Fix more tests that fail when run in parallel on the farm	2013-03-12 16:53:30 -04:00
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