gatk3的最后一个经典版本3.8

Christopher Hartl b59948709f Code improvements re: JIRA GSA-510. Trio class migrated into the Samples package - because the trio structure is so ubiquitously used, it makes sense, I think, to have a class which imposes the structure on the samples. Existing functions which slightly duplicated the getTrios() method look like they have bugs. These functions are now deprecated. ... A number of functions int he sampleDB looked to be assuming that samples could not share IDs (e.g. sample IDs are unique, so a sample present in two families could not be represented by multiple Sample objects). Added an assertion in the SampleDBBuilder to document/test this assumption. MVLikelihoodRatio now uses the trio methods from SampleDB.		2012-08-25 08:48:27 -07:00
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	Code improvements re: JIRA GSA-510. Trio class migrated into the Samples package - because the trio structure is so ubiquitously used, it makes sense, I think, to have a class which imposes the structure on the samples. Existing functions which slightly duplicated the getTrios() method look like they have bugs. These functions are now deprecated.	2012-08-25 08:48:27 -07:00
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