gatk3的最后一个经典版本3.8

Mark DePristo 3afbc50511 More BCF2 improvements ... -- Refactored setting of contigs from VCFWriterStub to VCFUtils. Necessary for proper BCF working -- Added VCFContigHeaderLine that manages the order for sorting, so we now emit contigs in the proper order. -- Cleaned up VCFHeader operations -- BCF now uses the right header files correctly when encoding / decoding contigs -- Clean up unused tools -- Refactored header parsing routines to make them more accessible -- More minor header changes from Intellij		2012-05-24 10:56:52 -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	More BCF2 improvements	2012-05-24 10:56:52 -04:00
settings	Rev. tribble to v101 with another putative open file leak fix	2012-05-04 15:40:41 -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	build system overhaul	2012-05-17 15:16:29 -04:00
ivy.xml	Not Nexus. Need new name. Navel?	2012-05-24 10:11:58 -04:00