gatk3的最后一个经典版本3.8

andrewk bef475778f - Updated --hapmap switch to --hapmap-chip to reflect the data being chip data for an individual rather than population allele frequency data in Hapmap ... - Corrected some bugs to get metrics logging working - Added a switch --force_1base_probs to ignore 4-base probalities if they exist git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@287 348d0f76-0448-11de-a6fe-93d51630548a		2009-04-03 17:32:31 +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	- Updated --hapmap switch to --hapmap-chip to reflect the data being chip data for an individual rather than population allele frequency data in Hapmap	2009-04-03 17:32:31 +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