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gatk3的最后一个经典版本3.8
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Java 95.8%
Scala 3.8%
R 0.2%
JavaScript 0.1%
 
 
 
 
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droazen 80d547ae71 Fix for bug GSA-445: Sequence dictionary validation can be very slow with 
large numbers of contigs. SequenceDictionaryUtils.getCommonContigsByName() was
running in O(n^2) time due to poor choice of data structure -- modified it to
run in O(n) time. Also removed an unnecessary O(n log n) step at another stage
in the sequence dictionary validation process. In tests with a 181,813-entry
sequence dictionary, runtime improved from an average of 21.4 minutes to 45.1
seconds.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5604 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-04-08 18:33:10 +00:00
R Misc changes 2011-02-26 15:35:49 +00:00
analysis/depristo Scripts for creating S3 IGV account 2011-04-02 13:39:47 +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 Fix for bug GSA-445: Sequence dictionary validation can be very slow with 2011-04-08 18:33:10 +00:00
lua forgot to remove a debug line. 2011-02-15 16:25:48 +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 Fixed inclusion of GATKEngine into the Queue package. 2011-04-01 17:45:46 +00:00
perl 2 more scripts I found helpful in syncing (and cleaning up) the 1000G mirror 2011-02-22 04:17:36 +00:00
python A helper script that will take a list of bams, a list of case sample IDs, and a list of control sample IDs, and generate a sample meta data yaml (which includes the bamfiles) 2011-03-21 16:11:55 +00:00
ruby accidentally commited an old tool 2010-08-25 15:42:02 +00:00
scala Minor bug fixes 2011-04-08 17:30:40 +00:00
settings Revved Picard to access new flag to disable mmap for bam indices. Only added a 3% speed boost but the mmap was added to the heap count, making it harder to specify/restrict the total resident memory size in LSF. Specifying -Xmx4g will now stay much closer to 4g resident memory usage versus bumping up to 9g when accessing 900 x ~8Mb bai's. 2011-04-01 01:40:41 +00:00
shell Useful utility for looking at the file size of GSA file systems 2011-04-02 03:47:27 +00:00
testdata ReplaceReadGroups. Fixes BAM files without read group info. MissingReadGroup points people to this tool now. Please point users on the forum to this tool now. Will migrate to Picard. 2011-02-21 14:02:41 +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 Modified the buildfile and help extractor doclet so that help text is only 2011-04-07 18:40:53 +00:00
ivy.xml Added commons math, for Kristian. 2011-02-14 18:57:21 +00:00