gatk3的最后一个经典版本3.8

Mark DePristo 0f4328f6fe Basic kmer error correction algorithm xfor the HaplotypeCaller ... -- Error correction algorithm for the assembler. Only error correct reads to others that are exactly 1 mismatch away -- The assembler logic is now: build initial graph, error correct*, merge nodes*, prune dead nodes, merge again, make haplotypes. The * elements are new -- Refactored the printing routines a bit so it's easy to write a single graph to disk for testing. -- Easier way to control the testing of the graph assembly algorithms -- Move graph printing function to DeBruijnAssemblyGraph from DeBruijnAssembler -- Simple protected parsing function for making DeBruijnAssemblyGraph -- Change the default prune factor for the graph to 1, from 2 -- debugging graph transformations are controllable from command line		2013-03-20 22:54:36 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Basic kmer error correction algorithm xfor the HaplotypeCaller	2013-03-20 22:54:36 -04:00
public	HaplotypeCaller now has the ability to only consider the best N haplotypes for genotyping	2013-03-20 22:54:36 -04:00
settings	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
.gitignore	Fixing the licensing scripts	2013-01-26 13:42:49 -05:00
build.xml	Fix tests that were consistently or intermittently failing when run in parallel on the farm	2013-03-06 13:56:54 -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	Brought all of ReduceReads to fastutils	2013-02-23 22:53:23 -05:00