gatk3的最后一个经典版本3.8

delangel ed71e53dd4 1) Initial complete version of VCF4 writer. There are still issues (see below) but at least this version is fully functional. It incorporates getting rid of intermediate VCFRecord so we now operate from VariantContext objects directly to VCF 4.0 output. ... See VCF4WriterTestWalker for usage example: it just amounts to adding vcfWriter.add(vc,ref.getBases()) in walker. add() method in VCFWriter is polymorphic and can also take a VCFRecord, lthough eventually this should be obsolete. addRecord is still supported so all backward compatibility is maintained. Resulting VCF4.0 are still not perfect, so additional changes are in progress. Specifically: a) INFO codes of length 0 (e.g. HM, DB) are not emitted correctly (they should emit just "HM" but now they emit "HM=1"). b) Genotype values that are specified as Integer in header are ignored in type and are printed out as Doubles. Both issues should be corrected with better header parsing. 2) Check in ability of Beagle to mask an additional percentage of genotype likelihoods (0 by default), for testing purposes. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3664 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-28 23:54:38 +00:00
R	This replaces tearsheet.r, neatens up graphics, and allows the script to be used in R's interactive environment	2010-06-24 01:02:58 +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	1) Initial complete version of VCF4 writer. There are still issues (see below) but at least this version is fully functional. It incorporates getting rid of intermediate VCFRecord so we now operate from VariantContext objects directly to VCF 4.0 output.	2010-06-28 23:54:38 +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	Updates to not depend on an environment variable to figure out where libraries are (helpful for installation at the Sanger).	2010-06-28 15:46:41 +00:00
python	Fixed error message	2010-06-28 14:50:28 +00:00
ruby	Adding the ruby directory, and a simple script to restart Bamboo	2009-12-03 22:48:48 +00:00
scala	Added "-bsubWait" where Queue waits for all the jobs to exit before exiting.	2010-06-28 19:52:17 +00:00
settings	Rev'ing Tribble with a special version that has excluded VCF 3.3	2010-06-25 18:20:51 +00:00
shell	Refactoring for a first version of scatter gather api with basic shell script implementations.	2010-06-22 18:39:20 +00:00
testdata	and add changes to the vcf used in testing	2010-06-25 02:56:02 +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	Refactoring for a first version of scatter gather api with basic shell script implementations.	2010-06-22 18:39:20 +00:00
ivy.xml	Refactoring for a first version of scatter gather api with basic shell script implementations.	2010-06-22 18:39:20 +00:00