gatk3的最后一个经典版本3.8

aaron e148a3ac61 added the ability to create interval lists directly from a ROD, using the command line arg '-BTI' (long name '--rodToIntervalTrackName'). The parameter to this arg is the name of the ROD track, which must be a track name specified in the -B option. ... Using this feature, sites covered by the target ROD will be iterated over. This list of intevals generated is merged with any intervals from the -L and -XL args, and the Walker is run over the resulting merged list. WARNING: for very large ROD's this can be costly. Consider this experimental for now. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3134 348d0f76-0448-11de-a6fe-93d51630548a		2010-04-08 05:14:41 +00:00
R	Moved CoverageStatistics to core. This will be (soon) renamed DepthOfCoverage; so please use CoverageStatistics	2010-03-29 13:32:00 +00:00
archive	CoverageStatistics has now replaced DepthOfCoverage -- old DoC is in the archive.	2010-04-01 16:27:23 +00:00
c	Reduce file handle usage.	2010-01-05 18:03:01 +00:00
doc	moved to wiki	2009-07-22 16:35:23 +00:00
java	added the ability to create interval lists directly from a ROD, using the command line arg '-BTI' (long name '--rodToIntervalTrackName'). The parameter to this arg is the name of the ROD track, which must be a track name specified in the -B option.	2010-04-08 05:14:41 +00:00
matlab	Another matlab script -- this time for making power and coverage plots over a specific gene region. Lots of fun file reading, string manipulation, and exploration of the set() function	2009-11-30 20:02:25 +00:00
packages	changed the depth of coverage walkers class name, and added a dependency in the packaging system so that RODs will all get imported.	2010-04-02 20:55:19 +00:00
perl	Passing just the single alternate allele to the converted maf on the recommendation of mike lawrence and kiran.	2010-03-17 19:08:37 +00:00
python	Make sure to convert non-integer chromosomes (M,X,Y) back from their corresponding integer representations (0,23,24) when writing in .bed format	2010-04-03 20:01:21 +00:00
ruby	Adding the ruby directory, and a simple script to restart Bamboo	2009-12-03 22:48:48 +00:00
scala/src	Scala walkers can now be build and run like any other walker in the GATK. Added the getUrlsForClasspath to PackageUtils, the Reflections package isn't getting the manifest files from jars in the classpath, and so we weren't seeing any walkers outside of the GenomeAnalysisTK.jar.	2009-11-02 06:02:41 +00:00
settings	Another round of cleanup and simplification in Picard -- Picard's unit tests	2010-03-31 01:02:59 +00:00
shell	Renaming error to getNegLog10PError(); added Cached clearing method to GL; SSG now has a CallResult that counts calls; No more Adding class to System.out, now to logger.info; First major testing piece (and general approach too) to unit testing of a walker -- SingleSampleGenotyper now knows how many calls to make on a particular 1mb region on NA12878 for each call type and counts the number of calls *AND* the compares the geli MD5 sum to the expected one!	2009-09-04 12:39:06 +00:00
testdata	a small dbsnp file for Tribble testing	2010-02-18 18:12:55 +00:00
build.xml	implementing a clean way to import the template files into the GATK jar (they should not always get bundled). All further resources should be added to the gatk.resources path id in the build script.	2010-03-30 04:20:19 +00:00
ivy.xml	Modified the report system based on Ryan's feedback: tables are now created independently to avoid the permutation problem when they were all compressed in rows, and removed our dependency on FreeMarker. The Grep format stays the same.	2010-04-07 20:39:55 +00:00