gatk3的最后一个经典版本3.8

David Roazen a7cb599945 Require a minimum dcov value of 200 for Locus and ActiveRegion walkers when downsampling to coverage ... -Throw a UserException if a Locus or ActiveRegion walker is run with -dcov < 200, since low dcov values can result in problematic downsampling artifacts for locus-based traversals. -Read-based traversals continue to have no minimum for -dcov, since dcov for read traversals controls the number of reads per alignment start position, and even a dcov value of 1 might be safe/desirable in some circumstances. -Also reorganize the global downsampling defaults so that they are specified as annotations to the Walker, LocusWalker, and ActiveRegionWalker classes rather than as constants in the DownsamplingMethod class. -The default downsampling settings have not been changed: they are still -dcov 1000 for Locus and ActiveRegion walkers, and -dt NONE for all other walkers.		2013-05-29 12:07:12 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Require a minimum dcov value of 200 for Locus and ActiveRegion walkers when downsampling to coverage	2013-05-29 12:07:12 -04:00
public	Require a minimum dcov value of 200 for Locus and ActiveRegion walkers when downsampling to coverage	2013-05-29 12:07:12 -04:00
settings	Rev picard, sam-jdk, tribble, and variant to version 1.91.1453	2013-05-07 14:21:15 -04:00
.gitignore	Detect stuck lock-acquisition calls, and disable file locking for tests	2013-04-24 22:49:02 -04:00
build.xml	Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements	2013-05-10 19:00:33 -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	Brought all of ReduceReads to fastutils	2013-02-23 22:53:23 -05:00