gatk-3.8

gatk3的最后一个经典版本3.8

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kshakir 57a168c0db Added a header crediting the python script as a source. Looping over an arbitrary number of headers. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2804 348d0f76-0448-11de-a6fe-93d51630548a		2010-02-07 03:38:30 +00:00
R	Making the dotted quartile lines more clear.	2010-02-03 22:23:09 +00:00
archive	moving older versions of the oneoff project to archive, bye-bye	2010-02-04 19:46:27 +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 generic interfaces to RefMetaDataTracker to obtain VariantContext objects. More docs. Integration tests for VariantContexts using dbSNP and VCF. At this stage if you use dbSNP or VCF files only in your walkers, please move them over to the VariantContext, it's just nicer. If you've got RODs that implemented the old variation/genotype interfaces, and you want them to work in new walkers, please add an adaptor to VariantContextAdaptors in refdata package. It should be easy and will reduce burden in the long term when those interfaces are retired.	2010-02-06 16:26:06 +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	Bringing IndelGenotyper back to life	2010-02-03 20:12:49 +00:00
perl	Minor fix: removed use command that doesn't work in /bin/sh scripts.	2010-02-05 19:52:50 +00:00
python	Added a header crediting the python script as a source. Looping over an arbitrary number of headers.	2010-02-07 03:38:30 +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	New Picard and SAM-JDK with automatic sequence name truncation	2010-01-11 20:49:13 +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	GSA-182: Adding support for BED interval files.	2009-10-06 02:45:31 +00:00
build.xml	Fully qualify the target for the output file so that external build processes (aka firehose)	2010-01-26 23:06:30 +00:00
ivy.xml	New VariantFiltration.	2009-11-20 19:50:26 +00:00