gatk3的最后一个经典版本3.8

hanna 53fe9acf65 Make command-line arguments available in walker constructor, provide back door from ... walker into GATK itself, do some cleanup of output messages, and add some bug fixes. Command-line arguments in walkers are now feature-complete, but still a bit messy. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@203 348d0f76-0448-11de-a6fe-93d51630548a		2009-03-26 20:45:27 +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	Make command-line arguments available in walker constructor, provide back door from	2009-03-26 20:45:27 +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	Fix path issue generating javadocs.	2009-03-26 18:51:56 +00:00
ivy.xml	Prototype, buggy implementation of walker command-line arguments. Doesn't	2009-03-25 00:12:00 +00:00