gatk3的最后一个经典版本3.8

Mark DePristo 9e23c592e6 ReadBackedPileup cleanup ... -- Only ReadBackedPileupImpl (concrete class) and ReadBackedPileup (interface) live, moved all functionality of AbstractReadBackedPileup into the impl -- ReadBackedPileupImpl was literally a shell class after we removed extended events. A few bits of code cleanup and we reduced a bunch of class complexity in the gatk -- ReadBackedPileups no longer accept pre-cached values (size, nMapQ reads, etc) but now lazy load these values as needed -- Created optimized calculation routines to iterator over all of the reads in the pileup in whatever order is most efficient as well. -- New LIBS no longer calculates size, n mapq, and n deletion reads while making pileups. -- Added commons-collections for IteratorChain		2013-01-11 15:17:18 -05:00
licensing	Cleaning CRLF terminations in the licenses	2013-01-10 17:06:29 -05:00
protected/java	Near final cleanup of PileupElement	2013-01-11 15:17:17 -05:00
public	ReadBackedPileup cleanup	2013-01-11 15:17:18 -05:00
settings	Final r119 tribble jar	2012-11-02 14:30:33 -04:00
.gitignore	adding some directories to gitignore	2012-09-27 11:09:41 -04:00
build.xml	Updating Queue maven version to 0.0.2	2013-01-10 13:46:49 -05:00
intellij_example.tar.bz2	Removed the intellij files from the root and made an example package for new users. This allows users to start at the same page and then change it as they see fit without interfering with the repo (thanks guillermo!)	2012-09-27 11:04:56 -04:00
ivy.xml	ReadBackedPileup cleanup	2013-01-11 15:17:18 -05:00