gatk-3.8

gatk3的最后一个经典版本3.8

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depristo a51061fd96 Improved distributed processing analytics. Still not 100% ready for prime-time. More improvements incoming. Iterator claim now supports requests to obtain in a single atomic claim (one lock) multiple sequential shards, which radically reduces overhead. However, deadlocking is still possible... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5061 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-23 16:17:25 +00:00
R	Updating the file path for proper inclusion of the background in the tearsheet.	2011-01-22 19:15:33 +00:00
analysis/depristo/distributedGATK	continuing to push to get right answers for long-running jobs	2011-01-22 15:02:02 +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	Improved distributed processing analytics. Still not 100% ready for prime-time. More improvements incoming. Iterator claim now supports requests to obtain in a single atomic claim (one lock) multiple sequential shards, which radically reduces overhead. However, deadlocking is still possible...	2011-01-23 16:17:25 +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	Deleting old python code	2011-01-07 21:33:45 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	Script for calling indels in all phase 1 samples - VQSR part still needs work but raw calling is done	2011-01-22 14:07:10 +00:00
settings	Update Picard / sam-jdk at Tim's request.	2011-01-03 02:17:25 +00:00
shell	Cleaning up obsolete code.	2011-01-21 16:27:35 +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	Removed stochasticity from IndelRealigner by random sampling using and seed based on the read list.	2011-01-07 22:03:36 +00:00