dd228880ed
Partially implemented NewHotnessGenotypeLikelihoodsTest caused the tests to fail.
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Ouch! So hot it burned me.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1403 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-10 20:45:44 +00:00
a864c2f025
Updated polarized reference priors, need DiploidGenotypePriors class that is directly used by the NewHotness genotypelikelihoods, more bug fixes and refactoring, etc.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1390 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-07 19:00:06 +00:00
bbd7bec5db
Continuing cleanup of SSG. GenotypeLikelihoods now have extensive testing routines. DiploidGenotype supports het, homref, etc calculations. SSG has been cleaned up to remove old garbage functionality. Also now supports output to standard output by simply omitting varout
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1387 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-05 22:25:30 +00:00
48713e154c
Windowed access to the reference.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1383 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-05 16:29:15 +00:00
21d1eba502
Cleaned division of responsibilities between arguments to map function. Reference has been changed
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from an array of bases to an object (ReferenceContext), and LocusContext has been renamed to reflect
the fact that it contains contextual information only about the alignments, not the locus in general.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1376 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-04 21:01:37 +00:00
bca894ebce
Adding the intial changes for the new Genotyping interface. The bullet points are:
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- SSG is much simpler now
- GeliText has been added as a GenotypeWriter
- AlleleFrequencyWalker will be deleted when I untangle the AlleleMetric's dependance on it
- GenotypeLikelihoods now implements GenotypeGenerator, but could still use cleanup
There is still a lot more work to do, but this is a good initial check-in.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1335 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-29 19:43:59 +00:00
7a13647c35
Support for specifying SAMFileReaders and SAMFileWriters as @Arguments directly. *Very*
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rough initial implementation, but should provide enough support so that people can stop
creating SAMFileWriters in reduceInit.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1332 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-29 16:11:45 +00:00
2db86b7829
Move the cleaned read injector test from playground to core. Remove CovariateCounterTest's dependency on the CleanedReadInjector. Start doing a bit of cleanup on the CLP's FieldParsers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1312 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-24 19:44:04 +00:00
0b16253db3
an iterator to fix the problem where read-based interval traversals are getting duplicate reads because reads span the two intervals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1305 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-23 23:59:48 +00:00
b4adb5133a
GLF rod as a AllelicVariant object.
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2009-07-21 00:55:52 +00:00
9ecb3e0015
adding GLFRods with tests and some other code changes
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2009-07-15 15:30:19 +00:00
d86717db93
Refactoring of the traversal engine base class, I removed a lot of old code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1209 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-09 21:57:00 +00:00
da4d26b1ea
Enum support for command-line argument system, and some cleanup for hacks to the CleanedReadInjector that were required because Enum support was missing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1199 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 20:26:16 +00:00
433ad1f060
Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1196 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 18:49:08 +00:00
d8fbb2b62c
Refactoring; make a better home for the MalformedReadFilteringIterator.
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2009-07-08 16:54:20 +00:00
f6a273a537
other fixes for some broken unit tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1181 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-07 05:53:13 +00:00
033bafe7a1
fixed sam by reads test for the new filtering code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1180 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-07 05:45:50 +00:00
b9d533042e
Two-tailed HardyWeinberg test implemented. VariantEval now separate violations from summary outputs for clarity; Fixing problems with CovariateCounterTest and TabularRodTest
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1177 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-06 22:02:04 +00:00
bc17ff567a
When you get the reference string for a read that is mapped partially off the end of a contig, the string is masked with X's for base positions without corresponding reference positions. Now with a test case!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1156 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-02 14:15:50 +00:00
9b182e3063
Prep for documenting command-line arguments: delete some arguments that don't make sense any more given
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the state of the traversals and GATK input requirements: all_loci (replaced by walker annotation), max
OTF sorts (bam files must be sorted and indexed), threaded io (replaced by data sharding framework).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1144 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 18:23:35 +00:00
03f8177a53
When you get the reference string for a read that is mapped partially off the end of a contig, the string is masked with X's for base positions without corresponding reference positions.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1121 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-29 20:51:55 +00:00
1dcababad1
a fix to make the test run
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1120 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-29 20:24:32 +00:00
5289230eb8
Version 0.2.1 (released) of the TableRecalibrator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1108 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 22:50:55 +00:00
ad3a3aa350
First pass at passing lists of files / lists of interval arguments work. Note that the interval
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ROD system will throw up its hands and not deal with intervals at all if multiple interval files
are passed in (see JIRA GSA-95).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1105 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 20:44:23 +00:00
0a16519aa2
a couple of additions to the tests, plus a change to the artificial resource pool to support the queryContained flag
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1099 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 18:30:32 +00:00
5b1c23a7f2
changes to fix and test the interval based traversals
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1095 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 17:54:15 +00:00
ef546868bf
Pooling of unmapped reads -- improves runtime of files with tons of unmapped reads by an order of magnitude.
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Desperately needs cleanup.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1080 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-23 23:48:06 +00:00
bcb64d92e9
Aaron: 1, GenomeLoc: 0. I changed our GenomeLoc class, seperating the creation of a genome loc (with the reference setup) to a parser class. GenomeLoc now just represents the actual genomic postion. The constructors are now package-protected (to enforce using the parser), but we may want to expose some constructors in the future.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1069 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-22 14:39:41 +00:00
8ac40e8e2d
Updated version of the recalibration tool
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1060 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-19 17:45:47 +00:00
6ee64c7e43
added changes to support alec toUnmappedRead seek. Huge improvements (orders of magnitude) in unmapped read performance.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1021 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-16 22:15:56 +00:00
647b8a1ab0
Fix TabularROD printing and testing so Aaron stops nagging me.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1016 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-16 15:49:26 +00:00
71e3825fa1
First pass of a walker for Eric that searches through an input BAM file for unclean reads, injecting the cleaned reads in their place and outputting the composite result.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@989 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 20:18:13 +00:00
63b5c12cbd
Changed dataSources to datasources, to be consistant with the rest of our package names. Also, this makes me champion in the largest check-in contest.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@985 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 18:13:22 +00:00
195b4ea7b4
a rename for consistancy of Sam to SAM, creating a genotype utils dir, and moving the GLF code into it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@984 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 17:46:06 +00:00
ec2f015447
fixed a bunch of comments and license headers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@964 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 14:10:46 +00:00
dc6a9ca196
Pooling resources to lower memory consumption.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@962 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 13:39:32 +00:00
36c98b9d6c
added tools to test read based traversals using the artificial in-memory SAM file tools, and testing of the PrintReadsWalker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@957 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 01:52:25 +00:00
a8a2d0eab9
added support for the -M option in traversals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@935 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-08 15:12:24 +00:00
819862e04e
major restructuring of generalized variant analysis framework. Now trivally easy to add additional analyses. Easy partitioning of all analyses by features, such as singleton status. Now has transition/transversional bias, counting, dbSNP coverage, HWE violation, selecting of variants by presence/absense in dbs. Also restructured the ROD system to make it easier to add tracks. Also, added the interval track -- if you provide an interval list, then the system autoatmically makese this available to you as a bound rod -- you can always find out where you are in the interval at every site. Python scripts improved to handle more merging, etc, into population snps.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@918 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-05 23:34:37 +00:00
109bef6c08
We're no longer in the read-dropping business.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@901 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 22:37:51 +00:00
5e8c08ee63
Update to latest version of picard. Change imports in all classes dependent on picard public from import edu.mit.broad.picard... to import net.sf.picard...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@849 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-28 20:13:01 +00:00
a11bf0f43e
Basic unit tests for ReferenceOrderedView, ShardDataProvider. Addressing GSA-25.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@844 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 21:15:01 +00:00
3c3cd5bb64
Moving some of the data sharding around. A new shard catagory now exits, INTERVAL. This saved a lot of code that was mirroring the same approach in both the read and locus shard strategies.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@840 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 18:24:31 +00:00
8edba13ded
Unit tests for the reference views. Partially addresses GSA-25.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@833 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 17:49:45 +00:00
d994544c47
Added back end code support for Sharding based on genomic location for reads. Changed the sharding
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code to take GenomeLocSortedSet instead of a list<GenomeLoc>, and added a bunch of much simplier
and cleaner test cases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@816 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 20:57:46 +00:00
2a5be1debe
Cleanup in datasources.providers namespace. Make it easier for others writing traversal engines to use.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@803 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 19:12:00 +00:00
d61a5261c1
Better integration of reference-ordered data into the data sharding system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@779 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 20:09:32 +00:00
2c4de7b5c5
Switch TraverseByLoci over to new sharding system, and cleanup some code in passing read files along
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the pathway from command line to traversal engine.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@727 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-15 21:02:12 +00:00
7834b969b4
Better interface to the tabular ROD, now makes writing files easier. Also has corresponding test files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@719 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 23:20:11 +00:00
50f32b7f61
Added a shard strategy for the reduce-by-interval traversals. Also fixed bugs that I found along the way.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@718 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 21:20:18 +00:00
8e9e2f4502
Revised ROD system. Split the system in Basic type and interface. Enabled more control over rod accessing, including an initialize() function to fetch headers and other options from the file. Added general tabular rod, which has a named columns and supports a map<String,String> interface. Comes with shiny new Junit system for RODs. Also, added simple python script for accessing picard data.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@716 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 21:06:28 +00:00
7aa90757ac
Moved the iterators over to the StingSAMIterator interface. This will help us ensure that iterators that need to be closed get closed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@702 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:52:18 +00:00
0215905bb6
Added an adapter class, that will adapt plain iterators and closeable iterators of SAMRecords into STingSAMIterators. Also unit tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@697 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 15:17:32 +00:00
d14cab0be7
Added IterableLocusContextQueue and test. Cleaned up tests, adding BaseTest where it didn't exist. Enhanced test runner to run only classes ending in ...Test.java, so that utility classes can sit alongside the tests but won't be run by JUnit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@693 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-13 21:32:05 +00:00
12ae3a22b6
Break locus context data access providers into modular components in preparation for traverse by loci.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@689 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-13 18:51:16 +00:00
862b8a6787
intervals_file + genome_loc => intervals.
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2009-05-12 01:04:18 +00:00
ff1b92acc4
Switch over to the GenomeAnalysisEngine/CommandLineGATK system from the GenomeAnalysisTK code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@655 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 22:05:58 +00:00
898f65547e
Added code to split GenomeAnalysisTK.java into an object concerned with loading command line args, and one that runs the engines. This will allow us to run the GATK from other tools (like Matlab). Also some cleanup to seperate out the legacy traversals and the new style traversals. This is not live yet, and any modifications you need should be made to GenomeAnalysisTK.java for now.
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2009-05-11 02:07:20 +00:00
6e394490cb
Cleanup in preparation for ByLoci traversal. Also did some work minimizing unit tests.
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2009-05-08 21:27:54 +00:00
0aba688e6f
Added a interface that all our SAMRecord iterators should try to code to. This is in the effort to keep our code generic
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2009-05-06 21:40:41 +00:00
70afda12c4
Cut the test time down
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2009-05-05 22:05:51 +00:00
f5880109a7
Added TraverseReads test, some bug fixes discovered in the traversal test
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2009-05-05 20:36:00 +00:00
09b0b6b57d
Fixes to try and speed up unmapped read traversals. Still not nearly as fast as they should be, but the next step would be to modify samtools code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@592 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 18:17:07 +00:00
9f5f6f9bc7
N-way parallelism. Works for small test cases. Untested for large test cases.
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-Needs more comprehensive unit testing.
-Needs some basic refactoring.
-Needs rethink of interface boundaries.
-Needs to play more nicely in the /tmp sandbox.
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2009-05-01 19:34:09 +00:00
63403d32cd
Changes to the interface to the simple data source rippled out to a bunch of files.
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2009-04-30 20:35:56 +00:00
19e4e97f21
Add tag to ignore node class.
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2009-04-30 20:27:34 +00:00
7f173af2ea
Encapsulate output tracking a bit.
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2009-04-30 15:12:13 +00:00
95d10ba314
Sketch of hierarchical reduce process, with unit tests for some core classes. Requires breakout of inner classes, testing.
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2009-04-29 20:26:16 +00:00
6b02248298
moved the test cases out of the GenomeAnalysisTK code and into a JUnit test case
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2009-04-28 21:49:17 +00:00
0720d248ce
Adding the test case for by reads sharding of BAM data sources
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@509 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 18:01:22 +00:00
180ff13290
Added a bunch of changes to support the new MicroManager code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@431 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 18:29:38 +00:00
6db9127f90
Added changes to shattering, refactored SAMBAM into SAM
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@426 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 13:52:56 +00:00
e6fb122d7d
Added some fixes and new iterator tests
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--This lin e, and those below, will be ignored--
A gatk/iterators
AM gatk/iterators/BoundedReadIteratorTest.java
M gatk/dataSources/simpleDataSources/SAMBAMDataSourceTest.java
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@420 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 22:19:36 +00:00
96248cdec4
Added some output to all the classes, including build in runtime analysis
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@411 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 19:14:53 +00:00
0629f79049
Moved fasta support files into their own package.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@408 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 18:13:23 +00:00
88ebf1a05b
Fied some documentation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@406 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 17:41:38 +00:00
4b3578e1de
Added the base test case, fixed the rest of the test cases to follow suit. Added more verbose output to ant for junit tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@403 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 17:11:38 +00:00
eb4b4a053b
A bunch of updates to the SAM/BAM data source, along with test cases for the merging of multiple files (it works!).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@399 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 14:19:20 +00:00
887adcfc7f
Some minor fixes to the last check-in
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@387 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 18:24:51 +00:00
9afa101465
Add interval support to the
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.__ __ __
_____| |__ _____ _/ |__/ |_ ___________
/ ___/ | \\__ \\ __\ __\/ __ \_ __ \
\___ \| Y \/ __ \| | | | \ ___/| | \/
/____ >___| (____ /__| |__| \___ >__|
\/ \/ \/ \/
classes!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@352 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 21:23:43 +00:00
8e2f5471a1
Some cleanup to the data source, and another JUnit test case.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@344 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 14:58:05 +00:00
d517245beb
Fixes for shattering, added JUnit test case
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@332 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 16:37:34 +00:00
hanna
depristo
aaron
ebanks