gatk-3.8

gatk3的最后一个经典版本3.8

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hanna c806ffba5f Switching over DownsamplingLocusIteratorByState -> LocusIteratorByState. Some operations will not be as fast as they could be because the workflow is currently merge sam records (sharding) -> split sam records (LocusIteratorByState) -> merge records (LocusIteraotorByState) -> split records (StratifiedAlignmentContext), but this will be fixed when StratifiedAlignmentContext is updated to take advantage of the new functionality in ReadBackedPileup. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3599 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-21 02:11:42 +00:00
R	This script produces tearsheet and data processing report figures and tables when given Squid and Firehose produced data	2010-06-18 21:36:29 +00:00
archive	Retiring multi-sample genotyper	2010-05-20 14:11:11 +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	Switching over DownsamplingLocusIteratorByState -> LocusIteratorByState. Some operations	2010-06-21 02:11:42 +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	Update to the latest rev of the picard sharding patch. Includes updates reflecting	2010-06-06 20:33:21 +00:00
perl	Stupid cent_os doesn't allow old style 'sort' conventions. Updating liftover script...	2010-06-17 13:44:03 +00:00
python	Fixed typo	2010-06-15 21:17:14 +00:00
ruby	Adding the ruby directory, and a simple script to restart Bamboo	2009-12-03 22:48:48 +00:00
scala/src	Fix for a reflection issue with generic types.	2010-06-16 15:58:38 +00:00
settings	GATK now uses a optimized indexing scheme in Tribble. 5x or more performance gain on files with many genotypes. Updated integrationtest that was failing and was clearly wrong. DB=; isn't a valid annotation.	2010-06-19 21:36:41 +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
LICENSE	Adding a license to the root directory in case BOSC checks for one. Has the	2010-04-20 16:04:29 +00:00
build.xml	Removing these utilities as part of a hostage negotation with Matt. Can I have my journal club paper now?!	2010-06-11 21:41:29 +00:00
ivy.xml	Replaced pattern matched pipeline spec with annotated objects.	2010-06-15 04:43:46 +00:00