gatk-3.8

gatk3的最后一个经典版本3.8

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asivache ea8d5c7077 Some internal refactoring. Now "safely" ignores duplicate records (NOT duplicate reads but rather malformed bam files!) resulting from the bug/feature in CleanedReadInjector. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1949 348d0f76-0448-11de-a6fe-93d51630548a		2009-10-30 17:50:51 +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	Created walkers for alignment, validation.	2009-10-30 15:04:07 +00:00
doc	moved to wiki	2009-07-22 16:35:23 +00:00
java	Some internal refactoring. Now "safely" ignores duplicate records (NOT duplicate reads but rather malformed bam files!) resulting from the bug/feature in CleanedReadInjector.	2009-10-30 17:50:51 +00:00
packages	added IndelGenotyperV2Walker	2009-10-29 20:07:31 +00:00
perl	/tmp is failing...	2009-10-08 18:13:49 +00:00
python	Faster grepping	2009-10-30 16:59:17 +00:00
scala/src	Major code refactoring:	2009-10-20 14:58:04 +00:00
settings	Bumping version of Picard for firehose compatibility.	2009-10-16 19:38:56 +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	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	Delete duplicate jgrapht reference.	2009-10-29 17:38:01 +00:00