gatk-3.8

gatk3的最后一个经典版本3.8

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asivache 43812a28fc If among all the multiple alignments for the given read we have 'unmapped' ones (can happen with bwa 0.5.7 and maybe later versions), then discard the latters and keep only the mapped ones. Keep 'unmapped' only if its the only alignment available. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5090 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-26 20:07:08 +00:00
R	Reformated backdrop--removed the date	2011-01-26 18:25:59 +00:00
analysis/depristo/distributedGATK	An apparently robust implementation of the file locking for distributed computation, using Lucene's file creation locking approach. It is worth trying out for those with large-scale, high-cost data sets. Details and discussion at group meeting on Wednesday. Some cleanup still needed.	2011-01-26 13:45:40 +00:00
archive	Moving GLF code to archive	2011-01-15 22:42:42 +00:00
c	Bug fixes for the bwa aligner and changes to support compiling against newer releases of the bwa code base.	2010-12-17 14:49:15 +00:00
doc	removing the custom reflections library from the libs, and adding a release version. Hopefully this will fix the problem Menachem has been seeing with random JVM crashes. Also	2010-08-19 00:42:37 +00:00
java	If among all the multiple alignments for the given read we have 'unmapped' ones (can happen with bwa 0.5.7 and maybe later versions), then discard the latters and keep only the mapped ones. Keep 'unmapped' only if its the only alignment available.	2011-01-26 20:07:08 +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	Adding the native jna support libraries from the jna.jar to the Queue package jar.	2011-01-08 10:48:30 +00:00
perl	Fixed bug that required users to use the recordOriginalLocation option	2011-01-05 23:12:14 +00:00
python	A quick python script to give the status of the projects in the humgen/gsa-pipeline/ directory	2011-01-25 15:21:50 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	Disabled FCPTest whilst we figure out where the C426 bams went.	2011-01-26 05:11:57 +00:00
settings	Update Picard / sam-jdk at Tim's request.	2011-01-03 02:17:25 +00:00
shell	V3 of the distributed GATK. High-efficiency implementation. Support for status tracking for debugging and display. Still not safe for production use due to NFS filelock problem. V4 will use alternative file locking mechanism	2011-01-24 16:45:07 +00:00
testdata	VQSR now operates on LOD scores in the INFO field directly, and doesn't adjust the QUAL field. New format for tranches file uses LOD score. Old file format no longer supported. log10sumlog10() function, a very useful utility in MathUtils. No more ExtendedPileupElement! Robust math calculations in GMM so that no infinities are generated! HaplotypeScore refactored to enable use of filtered context. Not yet enabled... InferredContext getDouble and getInteger arguments now parse values from Strings if necessary	2010-11-15 22:19:22 +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	FASTQ directory is gone	2011-01-13 15:16:06 +00:00
ivy.xml	Adding lucene dependency for file locking -- may be removed in the near future	2011-01-24 18:59:42 +00:00