gatk3的最后一个经典版本3.8

delangel 473ec91633 a) Bug fix in VCFHeader parsing - Info fields were not being parsed properly, with the result that the Count field was not being properly displayed in records (e.g. if Count=0 for a particular field, the INFO tag was still being displayed as ...;Field=x;... instead of ...;Field;... ... b) Bug fixes and update to how we represent indels and other complex events in a VariantContext object. Convention is now that all events are left aligned, with the first variant context location marking the common base before an event occurs. However, alleles in a VC don't have the common base in all VC's. Two new functions are now part of VariantContextUtils: CreateVariantContextWithPaddedAlleles and CreateVariantContextWithTrimmedAlleles. Both take a VC as an input and create a VC as an output. Main flow is that a VCF reader would create a VC with trimmed alleles, all walkers would ideally work with these trimmed alleles, and then the VCF writer would pad back the alleles before writing. However, there are special cases where we need to pad alleles like for example when merging/combining VC's. Pending issues: - PED and DBSNP RODs have to be updated to create VC's for indels following the convention above. Changes will go in after Tribble location is moved and things are tested. - Need to verify Indel genotyper and other modules that create VC's with indels.- Wiki page describing convention above and how walkers should interpret indel VC's still needs updating/detailing. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3850 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-22 02:36:45 +00:00
R	A very nice way of automatically plotting the results of a VariantEval run. All of the hard work is actually in the common R repository, gsacommons.R, including methods for creating a Venn diagram. It also provides a mechanism for the output of a VariantEval run to be loaded into a single list object.	2010-07-19 12:38:26 +00:00
archive	1. Refactoring of GenoypeWriters so that parallelization now works again with VCF4.0. We now have just a single reference to the old VCF classes, and that one will be purged soon.	2010-07-20 06:16:45 +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	a) Bug fix in VCFHeader parsing - Info fields were not being parsed properly, with the result that the Count field was not being properly displayed in records (e.g. if Count=0 for a particular field, the INFO tag was still being displayed as ...;Field=x;... instead of ...;Field;...	2010-07-22 02:36:45 +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	Add CountFunctionalVariants to local release (for firehose)	2010-07-17 01:36:16 +00:00
perl	1. Updated tests and added integration test for liftover code.	2010-07-12 17:58:18 +00:00
python	module for listing out samples for data processing and firehose reporting	2010-07-21 15:05:41 +00:00
ruby	Adding the ruby directory, and a simple script to restart Bamboo	2009-12-03 22:48:48 +00:00
scala	1KG Table 1 counting pipeline. Useful example	2010-07-17 22:30:56 +00:00
settings	updates to tribble with fixes for some bugs I've found in some new indexing code.	2010-07-20 22:08:04 +00:00
shell	a) Add input argument (-ncrate) to BeagleOutputToVCFWalker. If the genotype posterior error probability is higher than this threshold, we declare No-call at this genotype.	2010-07-06 18:33:28 +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	adding Ivy lines for findbug, and adding a build task (to run it locally you need to have installation of findbug). I'll put more information on the wiki when it's up and running.	2010-07-08 19:10:19 +00:00
ivy.xml	adding the annotations for findbugs as dependencies in the GATK. They have to be in the default config so that we can	2010-07-19 16:34:57 +00:00