gatk3的最后一个经典版本3.8

depristo d7c0bcc223 Reorganized GenomeLoc code to more clearly and better use the picard SequenceDictionary information. ... All GenomeLoc[] are not ArrayList<GenomeLoc> for clarity and consistency Parsing now recursively merges contiguous elements chr1:1-10;chr1:11-20 => chr1:1-20 Added support for TraversingByLoci over all reference positions specified by the provided location array. System dynamically determines which traversal system to use. Pileup now marks, very clearly, reference positions without covered reads. Made changes around the codebase to deal with new GenomeLoc structure. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@218 348d0f76-0448-11de-a6fe-93d51630548a		2009-03-28 20:37:27 +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	Reorganized GenomeLoc code to more clearly and better use the picard SequenceDictionary information.	2009-03-28 20:37:27 +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	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	Add targets to force build to core and force build to playground.	2009-03-27 22:32:44 +00:00
ivy.xml	Bump picard and samtools to latest.	2009-03-27 02:26:28 +00:00