gatk3的最后一个经典版本3.8

depristo c1abcfb014 Fixed problem where we were considering reads out of order because their stop positions where out of order, but with equal starts. This involved a change in the ordering feature of GenomeLoc, which now no longer sorts by both start and stop. So as long as the start positions are equal, things are considered "in order". Perhaps this isn't a good idea to change... ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@291 348d0f76-0448-11de-a6fe-93d51630548a		2009-04-03 19:53:33 +00:00
c	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
doc	rod's now have names. Use getName() to access it. Next step is better interface to accessing rods	2009-04-03 16:41:33 +00:00
java	Fixed problem where we were considering reads out of order because their stop positions where out of order, but with equal starts. This involved a change in the ordering feature of GenomeLoc, which now no longer sorts by both start and stop. So as long as the start positions are equal, things are considered "in order". Perhaps this isn't a good idea to change...	2009-04-03 19:53:33 +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	Bump picard and samtools to latest.	2009-03-27 02:26:28 +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	Removed now-useless FourBaseCaller jar target (FourBaseRecaller replaces it).	2009-04-02 22:13:51 +00:00
ivy.xml	Bump picard and samtools to latest.	2009-03-27 02:26:28 +00:00