gatk3的最后一个经典版本3.8

Johan Dahlberg e9b9e2318c Fixed SortSam bug, for .done file ... The *.bai.done file for the .bai file was written in the run directory instead of in the specified output directory. Changing getName() to getAbsolutePath() fixes this. Signed-off-by: Joel Thibault <thibault@broadinstitute.org>		2012-10-09 16:25:18 -04:00
licensing	Revert unintentional license change	2012-08-09 17:10:47 -04:00
protected/java	Don't allow triggering of polyploid consensus creation in regions where there is more than one het, as it just doesn't work properly. We could probably refactor at some point to make it work, but it's not worth doing that now (especially as it should be rare to have multiple proximal known hets in a single sample exome).	2012-10-07 16:32:48 -04:00
public	Fixed SortSam bug, for .done file	2012-10-09 16:25:18 -04:00
settings	Updating cofoja to the latest version	2012-08-09 16:36:18 -04:00
.gitignore	a few more useful git ignores	2012-09-01 11:08:36 -04:00
build.xml	Proper error handling in NanoScheduler	2012-09-19 17:03:13 -04:00
ivy.xml	Updating cofoja to the latest version	2012-08-09 16:36:18 -04:00