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Now builds examples, as I expected. GATKPaperGenotyper lives again. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5953 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-06-07 00:13:44 +00:00
parent 2901abf070
commit 311dfa0998
4 changed files with 3 additions and 40 deletions
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8
build.xml
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@ -252,7 +252,6 @@
description="compile the source">
<!-- Compile the java code from ${src} into build -->
<javac fork="true" memoryMaximumSize="512m" srcdir="${java.source.dir}" destdir="${java.classes}" debug="true" debuglevel="lines,vars,source" classpathref="external.dependencies" tempdir="${java.io.tmpdir}">
<exclude name="**/examples/**" />
<exclude name="**/playground/**" unless="include.playground"/>
<exclude name="**/oneoffprojects/**" unless="include.oneoffs"/>
<compilerarg value="-proc:none"/>
@ -268,7 +267,6 @@
<target name="gatk.contracts" depends="gatk.compile.source" description="create GATK contracts" if="use.contracts">
<javac fork="true" memoryMaximumSize="512m" srcdir="${java.source.dir}" destdir="${java.contracts}" debug="true" debuglevel="lines,vars,source" tempdir="${java.io.tmpdir}" >
<exclude name="**/examples/**" />
<exclude name="**/playground/**" unless="include.playground"/>
<exclude name="**/oneoffprojects/**" unless="include.oneoffs"/>
<classpath>
@ -679,10 +677,8 @@
<!-- needs to be if -->
<jvmarg value="-javaagent:lib/cofoja.jar"/>
<jvmarg value="-Dcom.google.java.contract.log.contract=false"/>
<!--
<jvmarg value="-Xdebug"/>
<jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/>
-->
<!-- <jvmarg value="-Xdebug"/> -->
<!-- <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/> -->
<classpath>
<path refid="external.dependencies" />
<pathelement location="${java.classes}" />

2
java/src/org/broadinstitute/sting/gatk/examples/papergenotyper/GATKPaperGenotyper.java → java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java
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@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.examples.papergenotyper;
package org.broadinstitute.sting.gatk.examples;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;

29
java/src/org/broadinstitute/sting/gatk/examples/papergenotyper/SimpleCall.java
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@ -1,29 +0,0 @@
package org.broadinstitute.sting.gatk.examples.papergenotyper;
import org.broadinstitute.sting.utils.GenomeLoc;
/**
* Created by IntelliJ IDEA.
* User: aaron
* Date: Nov 19, 2009
* Time: 2:07:25 AM
*
* This is a simple call class that stores the data for the per-locus calls of the GATKPaperGenotyper.
*
*/
class SimpleCall {
public String genotype;
public double LOD;
public GenomeLoc loc;
public char ref;
SimpleCall(GenomeLoc location, String gt, double lod, char reference) {
genotype = gt;
LOD = lod;
loc = location;
this.ref = reference;
}
public String toString() {
return String.format("%s\t%s\t%.4f\t%c", loc, genotype, LOD,ref);
}
}

4
java/src/org/broadinstitute/sting/gatk/examples/papergenotyper/package-info.java
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@ -1,4 +0,0 @@
/**
* @help.display.name The GATK paper's Bayesian genotyper
*/
package org.broadinstitute.sting.gatk.examples.papergenotyper;