gatk3的最后一个经典版本3.8

andrewk 0331cd8e95 Updated AlleleFrequency* classes to calculate separate lods for VarVsRef and BestVsNextBest mixture (qstar) theories; AFWMetrics now reports single sample performance w.r.t. Hapmap chip using the appropriate lod for gentoyping (BestVsNextBest) or variant / reference calling (VarVsRef). ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@196 348d0f76-0448-11de-a6fe-93d51630548a		2009-03-26 02:10:18 +00:00
c	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
doc	Added documentation for our coding standards.	2009-03-25 19:42:09 +00:00
java	Updated AlleleFrequency* classes to calculate separate lods for VarVsRef and BestVsNextBest mixture (qstar) theories; AFWMetrics now reports single sample performance w.r.t. Hapmap chip using the appropriate lod for gentoyping (BestVsNextBest) or variant / reference calling (VarVsRef).	2009-03-26 02:10:18 +00:00
python	Added Hapmap data track (using rodGFF class for GFF file format) to toolkit as a command line option, Hapmap metrics to AlleleFrequencyMetricsWalker, and a python Geli2GFF file converter.	2009-03-24 03:58:03 +00:00
settings	Update picard to work with new samtools.	2009-03-20 21:51:26 +00:00
shell	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
testdata	Skeleton of new directory structure.	2009-03-11 20:05:05 +00:00
build.xml	Prototype, buggy implementation of walker command-line arguments. Doesn't	2009-03-25 00:12:00 +00:00
ivy.xml	Prototype, buggy implementation of walker command-line arguments. Doesn't	2009-03-25 00:12:00 +00:00