gatk3的最后一个经典版本3.8

Guillermo del Angel 5a9a37ba01 Pool caller improvements: a) Log ref sample depth at every called site (will add more ref-related annotations later), b) Make -glm POOLBOTH work in case we want to genotype snp's and indels together, c) indel bug fix (pool and non-pool): prevent a bad GenomeLoc to be formed if we're running GGA and incoming alleles are larger than ref window size (typically 400 bb)		2012-06-29 11:08:16 -04:00
licensing	Remove old licensing	2012-04-25 12:23:08 -04:00
protected/java	Moving ReduceReads into protected	2012-06-25 17:01:33 -04:00
public	Pool caller improvements: a) Log ref sample depth at every called site (will add more ref-related annotations later), b) Make -glm POOLBOTH work in case we want to genotype snp's and indels together, c) indel bug fix (pool and non-pool): prevent a bad GenomeLoc to be formed if we're running GGA and incoming alleles are larger than ref window size (typically 400 bb)	2012-06-29 11:08:16 -04:00
settings	Testing of BCF codec	2012-05-24 10:57:01 -04:00
.gitignore	Minor additions to the shared .gitignore file, now that Mark has checked one in.	2011-10-26 12:24:28 -04:00
build.xml	ant fasttest: for when you just can't wait	2012-06-01 15:17:18 -04:00
ivy.xml	JEXL update	2012-06-21 15:17:21 -04:00