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Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Mark DePristo 2011-10-06 10:50:02 -07:00
parent 73f9d1f217 3961733590
commit ab357ef900
2 changed files with 55 additions and 3 deletions
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7
build.xml
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@ -548,8 +548,9 @@
<target name="vcf.jar" depends="gatk.compile,init.jar">
<jar jarfile="${dist.dir}/vcf.jar">
<fileset dir="${java.classes}">
<include name="**/utils/codecs/**/*.class"/>
<include name="**/utils/variantcontext/**/*.class"/>
<include name="org/broadinstitute/sting/utils/codecs/vcf/**/*.class"/>
<include name="org/broadinstitute/sting/utils/variantcontext/**/*.class"/>
<include name="org/broadinstitute/sting/gatk/refdata/SelfScopingFeatureCodec.class"/>
<include name="org/broadinstitute/sting/utils/exceptions/**"/>
<include name="org/broadinstitute/sting/utils/help/DocumentedGATKFeature.class"/>
</fileset>
@ -916,7 +917,7 @@
</target>
<!-- Our four different test conditions: Test, IntegrationTest, PerformanceTest, PipelineTest -->
<target name="test" depends="init.buildall,test.compile" description="Run unit tests">
<target name="test" depends="init.buildall,test.compile,vcf.jar" description="Run unit tests">
<condition property="ttype" value="*UnitTest" else="${single}">
<not><isset property="single"/></not>
</condition>

51
public/java/test/org/broadinstitute/sting/utils/variantcontext/VCFJarClassLoadingUnitTest.java 100644
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@ -0,0 +1,51 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.variantcontext;
import org.testng.annotations.Test;
import java.io.File;
import java.net.MalformedURLException;
import java.net.URI;
import java.net.URL;
import java.net.URLClassLoader;
/**
* Test to ensure that, given only the VCF jar and its expected dependencies, core VCF classes will load.
*/
public class VCFJarClassLoadingUnitTest {
@Test
public void testVCFJarClassLoading() throws ClassNotFoundException, MalformedURLException {
URI vcfURI = new File("dist/vcf.jar").toURI();
URI tribbleURI = new File("lib/tribble-24.jar").toURI();
ClassLoader classLoader = new URLClassLoader(new URL[] {vcfURI.toURL(),tribbleURI.toURL()}, null);
classLoader.loadClass("org.broadinstitute.sting.utils.variantcontext.VariantContext");
classLoader.loadClass("org.broadinstitute.sting.utils.codecs.vcf.VCFCodec");
classLoader.loadClass("org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec");
classLoader.loadClass("org.broadinstitute.sting.utils.codecs.vcf.VCFWriter");
classLoader.loadClass("org.broadinstitute.sting.utils.codecs.vcf.StandardVCFWriter");
}
}