gatk-3.8

gatk3的最后一个经典版本3.8

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asivache d804bdf210 New option: --maxReadsInRam . When using ON_DISK sorting option, the tool may still run out of memory in the regions of pathologically deep coverage because of the generous memory usage limit set in the underlying samtools' sorting sam writers. With this option, the user can lower the number of reads the writer keeps in memory before spilling them on disk. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2985 348d0f76-0448-11de-a6fe-93d51630548a		2010-03-11 21:15:03 +00:00
R	Eliminate the shell items, as FH will be calling this with /broad/tools/apps/R-2.72/bin/Rscript	2010-03-09 20:15:21 +00:00
archive	moving older versions of the oneoff project to archive, bye-bye	2010-02-04 19:46:27 +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	New option: --maxReadsInRam . When using ON_DISK sorting option, the tool may still run out of memory in the regions of pathologically deep coverage because of the generous memory usage limit set in the underlying samtools' sorting sam writers. With this option, the user can lower the number of reads the writer keeps in memory before spilling them on disk.	2010-03-11 21:15:03 +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	removing the package description for the VCF validator	2010-03-02 15:45:51 +00:00
perl	Band-Aid: changed the pointers from mike's home directory to a checkout of the last know working revision r7169 in my directory.	2010-03-07 04:19:01 +00:00
python	Make annotated VCF not be broken	2010-03-01 23:22:41 +00:00
ruby	Adding the ruby directory, and a simple script to restart Bamboo	2009-12-03 22:48:48 +00:00
scala/src	Scala walkers can now be build and run like any other walker in the GATK. Added the getUrlsForClasspath to PackageUtils, the Reflections package isn't getting the manifest files from jars in the classpath, and so we weren't seeing any walkers outside of the GenomeAnalysisTK.jar.	2009-11-02 06:02:41 +00:00
settings	adding a stripped down Tribble library for the start of integration	2010-02-17 21:29:25 +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	a small dbsnp file for Tribble testing	2010-02-18 18:12:55 +00:00
build.xml	In the new sharding system, if no read group is present, hallucinate one. Added	2010-03-07 23:01:34 +00:00
ivy.xml	adding a stripped down Tribble library for the start of integration	2010-02-17 21:29:25 +00:00