gatk3的最后一个经典版本3.8

Ryan Poplin d38f3a071f fixing typo in comments		2012-07-22 16:54:19 -04:00
licensing	Final final version of GATK beta license	2012-07-19 10:39:34 -04:00
protected/java	New function for merging nearby events into MNPs or complex substitutions. Added extensive unit tests.	2012-07-19 13:16:33 -04:00
public	a) Use new method to check for GATK Like, b) minor improvements to indel pool caller (more to come): brain-dead, quick way to limit number of alt alleles to genotype. We can't process too many alt alleles because of the combinatorial explosion of GL values with high ploidy, and some STR validation targets had up to 12 alt alleles, resulting of GL vectors of > 1e8 elements. Can't use pileup elements since typically not many alleles will be in one pileup, and different alleles will appear in different samples, TBD a nicer solution. c) Commit to posterity scala script for large scale validation calling, still work in progress	2012-07-19 10:24:08 -04:00
settings	Rev tribble to 110. Log is:	2012-06-26 15:28:32 -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	Change committest target to allow inheritance of properties	2012-07-18 12:45:51 -04:00
ivy.xml	Navel -> GXDB	2012-06-28 13:38:00 -04:00