gatk3的最后一个经典版本3.8

Guillermo del Angel aee66ab157 Big UG refactoring and intermediate commit to support indels in pool caller (not done yet). Lots of code pulled out of long spaghetti-like functions and modularized to be easily shareable. Add functionality in ErrorModel to count indel matches/mismatches (but left part disabled as not to change integration tests in this commit), add computation of pool genotype likelihoods for indels (not fully working yet in more realistic cases, only working in artificial nice pools). Lot's of TBD's still but existing UG and pool SNP functionality should be intact		2012-06-13 11:14:44 -04:00
licensing	Remove old licensing	2012-04-25 12:23:08 -04:00
protected/java/src/org/broadinstitute/sting	build system overhaul	2012-05-17 15:16:29 -04:00
public	Big UG refactoring and intermediate commit to support indels in pool caller (not done yet). Lots of code pulled out of long spaghetti-like functions and modularized to be easily shareable. Add functionality in ErrorModel to count indel matches/mismatches (but left part disabled as not to change integration tests in this commit), add computation of pool genotype likelihoods for indels (not fully working yet in more realistic cases, only working in artificial nice pools). Lot's of TBD's still but existing UG and pool SNP functionality should be intact	2012-06-13 11:14:44 -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	Final updates to integration tests for BCF2	2012-05-24 10:58:59 -04:00