gatk3的最后一个经典版本3.8

ebanks 19bfe43173 First pass at a unified caller, being checked in now so Mark can give feedback if he chooses and so Matt can debug issues with the ArgumentCollection class. ... Some notes: 1. This design should be flexible enough to include pooled calling (for now) after discussions with Chris. 2. Using the unified caller with the SingleSampleCalculationModel emits the exact same output as SSG over all of chr20 for NA12878. Additionally, when we include the "max deletions allowed at a locus" argument (so we don't try to call SNPs at deletion sites), it removed 233 SNP calls in chr20 that were clearly indel artficts. 3. The MultiSampleEMCalculationModel is still a work in progress and will be checked in later this week. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1740 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-29 16:48:15 +00:00
R	R script for selecting a variety of baits (using %GC content and normalized coverage) for Nanostring assessment from those used in the Agilent whole exome hybrid selection design.	2009-09-22 18:10:14 +00:00
c	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
doc	moved to wiki	2009-07-22 16:35:23 +00:00
java	First pass at a unified caller, being checked in now so Mark can give feedback if he chooses and so Matt can debug issues with the ArgumentCollection class.	2009-09-29 16:48:15 +00:00
packages	moving IndelGenotyper out from playground	2009-09-25 19:43:53 +00:00
perl	add wait id for 454	2009-09-22 01:41:58 +00:00
python	Detects unmapped (no bai) bam files and doesn't blow up	2009-09-25 12:56:28 +00:00
scala/src	support for scala walkers	2009-08-28 00:15:01 +00:00
settings	Switched to Reflections (http://code.google.com/p/reflections/) project for	2009-07-21 18:32:22 +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	Framework for ROD walkers -- totally experiment and not working right now	2009-09-12 19:13:15 +00:00
build.xml	changes to the variation class, updates to SSG, updated tests based on changes to the SSGenotypeCall, and added the ability to run a single integration test from using the build script.	2009-09-10 04:31:33 +00:00
ivy.xml	Switched to Reflections (http://code.google.com/p/reflections/) project for	2009-07-21 18:32:22 +00:00