gatk3的最后一个经典版本3.8

Mark DePristo 2472828e1c HC bug fixes: no longer create reference graphs with cycles ... -- Though not intended, it was possible to create reference graphs with cycles in the case where you started the graph with a homopolymer of length > the kmer. The previous test would fail to catch this case. Now its not possible -- Lots of code cleanup and refactoring in this push. Split the monolithic createGraphFromSequences into simple calls to addReferenceKmersToGraph and addReadKmersToGraph which themselves share lower level functions like addKmerPairFromSeqToGraph. -- Fix performance problem with reduced reads and the HC, where we were calling add kmer pair for each count in the reduced read, instead of just calling it once with a multiplicity of count. -- Refactor addKmersToGraph() to use things like addOrUpdateEdge, now the code is very clear		2013-03-26 10:12:24 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	HC bug fixes: no longer create reference graphs with cycles	2013-03-26 10:12:24 -04:00
public	Added support to reduce reads to Callable Loci	2013-03-21 15:53:04 -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