gatk3的最后一个经典版本3.8

Mauricio Carneiro 1466396a31 Diagnose target is outputting intervals out of order ... Problem ------- When the interval had no reads, it was being sent to the VCF before the intervals that just got processed, therefore violating the sort order of the VCF. Solution -------- Use a linked hash map, and make the insertion and removal all happen in one place regardless of having reads or not. Since the input is ordered, the output has to be ordered as well. Itemized changes -------------- * Clean up code duplication in LocusStratification and SampleStratification * Add number of uncovered sites and number of low covered sites to the VCF output. * Add new VCF format fields * Fix outputting multiple status when threshold is 0 (ratio must be GREATER THAN not equal to the threshold to get reported) [fixes #48780333] [fixes #48787311]		2013-05-13 11:50:22 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Diagnose target is outputting intervals out of order	2013-05-13 11:50:22 -04:00
public	New faster Smith-Waterman implementation that is edge greedy and assumes that ref and haplotype have same global start/end points.	2013-05-13 09:36:39 -04:00
settings	Rev picard, sam-jdk, tribble, and variant to version 1.91.1453	2013-05-07 14:21:15 -04:00
.gitignore	Detect stuck lock-acquisition calls, and disable file locking for tests	2013-04-24 22:49:02 -04:00
build.xml	Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements	2013-05-10 19:00:33 -04:00
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