gatk3的最后一个经典版本3.8

Mark DePristo 2996693c9f FisherStrand now computed with and without filtering low-qual bases, and least significant pvalue is kept ... -- Old way (filtering for Q > 17 bases) resulted in biased FS when the site was good but there was a systematic shift in the QUAL of REF and ALT between strands of the reads (sometimes happens) -- New way (taking all bases) was consistent with BaseQualRankSum and other tests, but there can be a lot of low qual reference bases on one strand in some techs (ION/PROTON/PACBIO) because of the preference for introducing an indel vs. a mismatch. -- This implementation allows us to have our cake and eat it to by computing both p-values, and taking the maximum one (i.e., least significant). -- No integration tests updated yet -- still exploring the consequences of this change		2012-08-28 08:06:47 -04:00
licensing	Revert unintentional license change	2012-08-09 17:10:47 -04:00
protected/java	HaplotypeCaller forbids BAQ	2012-08-24 13:25:05 -04:00
public	FisherStrand now computed with and without filtering low-qual bases, and least significant pvalue is kept	2012-08-28 08:06:47 -04:00
settings	Updating cofoja to the latest version	2012-08-09 16:36:18 -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	Convert external.build.dir and external.dist.dir back to paths	2012-08-15 23:04:10 -04:00
ivy.xml	Updating cofoja to the latest version	2012-08-09 16:36:18 -04:00