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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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hanna 8e36a07bea Convert GenomeLocParser into an instance variable. This change is required 
for anything that needs to be simultaneously aware of multiple references, eg
Queue's interval sharding code, liftover support, distributed GATK etc.  

GenomeLocParser instances must now be used to create/parse GenomeLocs.
GenomeLocParser instances are available in walkers by calling either

-getToolkit().getGenomeLocParser()
or
-refContext.getGenomeLocParser()

This is an intermediate change; GenomeLocParser will eventually be merged
with the reference, but we're not clear exactly how to do that yet.  This
will become clearer when contig aliasing is implemented.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4642 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-11-10 17:59:50 +00:00
R now prints a nice report, can be invoked from command line 2010-11-09 19:44:10 +00:00
archive Fisher exact makes a return. Seems to be working properly. Current tagged as a work in progress. Needs to take the filtered context to be truly correct. 2010-10-22 20:35:53 +00:00
c Reduce file handle usage. 2010-01-05 18:03:01 +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 Convert GenomeLocParser into an instance variable. This change is required 2010-11-10 17:59:50 +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 by request, an indexer tool to create Tribble style indexes outside of the GATK 2010-11-06 18:59:06 +00:00
perl Also removed contig intervals from the pipeline sanity check perl scsript. 2010-10-21 11:23:34 +00:00
python Simple pre-processing script for soapsnp files 2010-11-04 20:34:43 +00:00
ruby accidentally commited an old tool 2010-08-25 15:42:02 +00:00
scala Convert GenomeLocParser into an instance variable. This change is required 2010-11-10 17:59:50 +00:00
settings Added status email support with -statusTo. Will send emails on failure of an individual function or success/failure of the whole pipeline. 2010-10-14 15:58:52 +00:00
shell Inprocess functions by default now log what output files they are running for. 2010-10-07 19:08:02 +00:00
testdata Fixes for example bam files 2010-10-05 18:43:02 +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 GSA-413 Explicitly set all compilers to use 512m memory maximum instead of 64m default maximum and running them out of the ant process. 2010-11-09 19:32:19 +00:00
ivy.xml Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00