gatk-3.8

gatk3的最后一个经典版本3.8

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hanna 7087c2f422 Very simple integration tests for basic VCF streaming functionality. Rather than try to fork the integration test process to get a pipe source and sink, creates a new named pipe by Runtime.exec()ing the 'mkfifo' shell command. We'll see whether this proves to be a reliable method for testing streaming. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5028 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-20 04:38:54 +00:00
R	Adding the backdrop to the current version of the tearsheet so it is always available	2011-01-19 20:56:11 +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	Very simple integration tests for basic VCF streaming functionality.	2011-01-20 04:38:54 +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	Updated FCPTest to use the new path to fullCallingPipeline.q changed in r5017.	2011-01-19 21:43:43 +00:00
settings	Update Picard / sam-jdk at Tim's request.	2011-01-03 02:17:25 +00:00
shell	An example template for the shell script used to run the full calling pipeline on the broad system	2011-01-19 20:28:59 +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