zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Mauricio Carneiro 2011-10-18 15:23:05 -04:00
parent e12ffb6547 2125c4f38f
commit c27e2fb676
13 changed files with 281 additions and 95 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

158
build.xml
View File

@ -67,6 +67,8 @@
<!-- If running the 'package' task, this property controls the name of the xml file to package -->
<property name="package.xml.dir" value="${public.dir}/packages" />
<property name="package.output.dir" value="${dist.dir}/packages" />
<property name="staging.dir" value="staging" />
<property name="executable" value="GenomeAnalysisTK" />
<property environment="env"/>
@ -118,6 +120,16 @@
</fileset>
</path>
<path id="testng.dependencies">
<fileset dir="${lib.dir}">
<include name="jcommander*.jar"/>
<include name="guice*.jar"/>
<include name="junit*.jar"/>
<include name="bsh*.jar"/>
<include name="snakeyaml*.jar"/>
</fileset>
</path>
<path id="build.results">
<fileset dir="dist">
<patternset refid="dependency.mask" />
@ -509,7 +521,7 @@
docletpathref="doclet.classpath"
classpathref="external.dependencies"
classpath="${java.classes}"
additionalparam="${gatkdocs.include.hidden.arg} -private -build-timestamp &quot;${build.timestamp}&quot; -absolute-version ${build.version} -quiet -J-Xdebug -J-Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=5005"> <!-- -test to only do DocumentationTest walker -->
additionalparam="${gatkdocs.include.hidden.arg} -private -build-timestamp &quot;${build.timestamp}&quot; -absolute-version ${build.version} -quiet"> <!-- -test to only do DocumentationTest walker -->
<sourcefiles>
<union>
<fileset refid="all.java.source.files"/>
@ -829,10 +841,54 @@
<target name="test.compile" depends="init.usecontracts,test.java.compile,test.scala.compile" />
<path id="testng.default.classpath">
<path refid="external.dependencies" />
<pathelement location="${java.classes}" />
<pathelement location="${scala.classes}" />
<pathelement location="${java.contracts}" />
<pathelement location="${java.public.test.classes}" />
<pathelement location="${java.private.test.classes}" />
<pathelement location="${scala.public.test.classes}" />
<pathelement location="${scala.private.test.classes}" />
</path>
<path id="testng.gatk.releasetest.classpath">
<path refid="testng.dependencies" />
<path>
<fileset dir="${package.output.dir}">
<include name="**/${executable}.jar" />
</fileset>
</path>
<pathelement location="${java.contracts}" />
<pathelement location="${java.public.test.classes}" />
<pathelement location="${scala.public.test.classes}" />
<pathelement location="${scala.classes}" />
<path>
<fileset dir="${lib.dir}">
<include name="scala*.jar"/>
<include name="jna*.jar"/>
</fileset>
</path>
</path>
<path id="testng.queue.releasetest.classpath">
<path refid="testng.dependencies" />
<path>
<fileset dir="${package.output.dir}">
<include name="**/${executable}.jar" />
</fileset>
</path>
<pathelement location="${java.contracts}" />
<pathelement location="${java.public.test.classes}" />
<pathelement location="${scala.public.test.classes}" />
</path>
<!-- TEST -->
<macrodef name="run-test">
<attribute name="testtype"/>
<attribute name="outputdir"/>
<attribute name="classpath"/>
<attribute name="runfailed"/>
<sequential>
@ -853,6 +909,7 @@
<echo message="Sting: Running @{testtype} test cases!"/>
<taskdef resource="testngtasks" classpath="${testng.jar}"/>
<testng outputDir="@{outputdir}"
classpathref="@{classpath}"
haltOnFailure="false" failureProperty="test.failure"
verbose="2"
workingDir="${basedir}"
@ -865,16 +922,6 @@
<jvmarg line="${cofoja.jvm.args}"/>
<!-- <jvmarg value="-Xdebug"/> -->
<!-- <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/> -->
<classpath>
<path refid="external.dependencies" />
<pathelement location="${java.classes}" />
<pathelement location="${scala.classes}" />
<pathelement location="${java.contracts}" />
<pathelement location="${java.public.test.classes}" />
<pathelement location="${java.private.test.classes}" />
<pathelement location="${scala.public.test.classes}" />
<pathelement location="${scala.private.test.classes}" />
</classpath>
<classfileset dir="${java.public.test.classes}" includes="**/@{testtype}.class"/>
<classfileset dir="${java.private.test.classes}" erroronmissingdir="false">
@ -904,6 +951,10 @@
</sequential>
</macrodef>
<target name="test.init">
<property name="testng.classpath" value="testng.default.classpath" />
</target>
<target name="alltests">
<antcall target="test" inheritAll="false"/>
<antcall target="integrationtest" inheritAll="false"/>
@ -916,62 +967,81 @@
<antcall target="pipelinetest.public" inheritAll="false"/>
</target>
<target name="alltests.gatk.packagejar" depends="init.buildpublic,package">
<antcall target="test.public" inheritAll="false">
<param name="testng.classpath" value="testng.gatk.releasetest.classpath" />
</antcall>
<antcall target="integrationtest.public" inheritAll="false">
<param name="testng.classpath" value="testng.gatk.releasetest.classpath" />
</antcall>
</target>
<target name="alltests.queue.packagejar" depends="init.buildpublic,queue">
<antcall target="package" inheritAll="false">
<param name="executable" value="Queue" />
</antcall>
<antcall target="pipelinetest.public" inheritAll="false">
<param name="executable" value="Queue" />
<param name="testng.classpath" value="testng.queue.releasetest.classpath" />
</antcall>
</target>
<!-- Our four different test conditions: Test, IntegrationTest, PerformanceTest, PipelineTest -->
<target name="test" depends="init.buildall,test.compile,vcf.jar" description="Run unit tests">
<target name="test" depends="init.buildall,test.compile,vcf.jar,test.init" description="Run unit tests">
<condition property="ttype" value="*UnitTest" else="${single}">
<not><isset property="single"/></not>
</condition>
<run-test testtype="${ttype}" outputdir="${report}/${ttype}" runfailed="false"/>
<run-test testtype="${ttype}" outputdir="${report}/${ttype}" classpath="${testng.classpath}" runfailed="false"/>
</target>
<target name="test.public" depends="init.buildpublic,test"/>
<target name="integrationtest" depends="init.buildall,test.compile" description="Run integration tests">
<target name="integrationtest" depends="init.buildall,test.compile,test.init" description="Run integration tests">
<condition property="itype" value="*IntegrationTest" else="${single}">
<not><isset property="single"/></not>
</condition>
<run-test testtype="${itype}" outputdir="${report}/${itype}" runfailed="false"/>
<run-test testtype="${itype}" outputdir="${report}/${itype}" classpath="${testng.classpath}" runfailed="false"/>
</target>
<target name="integrationtest.public" depends="init.buildpublic,integrationtest"/>
<target name="performancetest" depends="init.buildall,test.compile" description="Run performance tests">
<target name="performancetest" depends="init.buildall,test.compile,test.init" description="Run performance tests">
<condition property="ptype" value="*PerformanceTest" else="${single}">
<not><isset property="single"/></not>
</condition>
<run-test testtype="${ptype}" outputdir="${report}/${ptype}" runfailed="false"/>
<run-test testtype="${ptype}" outputdir="${report}/${ptype}" classpath="${testng.classpath}" runfailed="false"/>
</target>
<target name="performancetest.public" depends="init.buildpublic,performancetest" />
<target name="pipelinetest" depends="init.buildall,test.compile" description="Run pipeline tests">
<target name="pipelinetest" depends="init.buildall,test.compile,test.init" description="Run pipeline tests">
<condition property="pipetype" value="*PipelineTest" else="${single}">
<not><isset property="single"/></not>
</condition>
<run-test testtype="${pipetype}" outputdir="${report}/${pipetype}" runfailed="false"/>
<run-test testtype="${pipetype}" outputdir="${report}/${pipetype}" classpath="${testng.classpath}" runfailed="false"/>
</target>
<target name="pipelinetest.public" depends="init.buildpublic,pipelinetest" />
<target name="pipelinetestrun" depends="init.buildall,test.compile" description="Run pipeline tests">
<target name="pipelinetestrun" depends="init.buildall,test.compile,test.init" description="Run pipeline tests">
<property name="pipeline.run" value="run"/>
<condition property="pipetype" value="*PipelineTest" else="${single}">
<not><isset property="single"/></not>
</condition>
<run-test testtype="${pipetype}" outputdir="${report}/${pipetype}" runfailed="false"/>
<run-test testtype="${pipetype}" outputdir="${report}/${pipetype}" classpath="${testng.classpath}" runfailed="false"/>
</target>
<target name="pipelinetestrun.public" depends="init.buildpublic,pipelinetestrun" />
<target name="failed-test" depends="init.buildall,test.compile">
<run-test testtype="${report}/*UnitTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/>
<target name="failed-test" depends="init.buildall,test.compile,test.init">
<run-test testtype="${report}/*UnitTest/testng-failed.xml" outputdir="${report}/failed_rerun" classpath="${testng.classpath}" runfailed="true"/>
</target>
<target name="failed-integration" depends="init.buildall,test.compile">
<run-test testtype="${report}/*IntegrationTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/>
<target name="failed-integration" depends="init.buildall,test.compile,test.init">
<run-test testtype="${report}/*IntegrationTest/testng-failed.xml" outputdir="${report}/failed_rerun" classpath="${testng.classpath}" runfailed="true"/>
</target>
<target name="failed-performance" depends="init.buildall,test.compile">
<run-test testtype="${report}/*PerformanceTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/>
<target name="failed-performance" depends="init.buildall,test.compile,test.init">
<run-test testtype="${report}/*PerformanceTest/testng-failed.xml" outputdir="${report}/failed_rerun" classpath="${testng.classpath}" runfailed="true"/>
</target>
<target name="failed-pipeline" depends="init.buildall,test.compile">
<run-test testtype="${report}/*PipelineTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/>
<target name="failed-pipeline" depends="init.buildall,test.compile,test.init">
<run-test testtype="${report}/*PipelineTest/testng-failed.xml" outputdir="${report}/failed_rerun" classpath="${testng.classpath}" runfailed="true"/>
</target>
<!-- ******************************************************************************** -->
@ -1029,14 +1099,14 @@
<!-- Unzip all classes from their current locations and assemble them in a staging directory -->
<target name="stage" description="stage files for distribution">
<mkdir dir="staging"/>
<mkdir dir="${staging.dir}"/>
<!--
HACK: Create the edu directory before EDU on case-insensitive mac filesystems.
The ivy dependency colt -> concurrent contains an EDU.oswego package which
BCEL doesn't even pull in but messes up edu.mit.broad.
-->
<mkdir dir="staging/edu"/>
<unjar dest="staging" overwrite="false">
<mkdir dir="${staging.dir}/edu"/>
<unjar dest="${staging.dir}" overwrite="false">
<fileset dir="${dist.dir}">
<patternset refid="dependency.mask" />
</fileset>
@ -1045,8 +1115,8 @@
<!-- Build a package consisting of all supporting files -->
<target name="package" depends="dist,stage" description="bundle up an executable for distribution">
<mkdir dir="dist/packages" />
<xslt destdir="dist/packages" style="${package.xml.dir}/CreatePackager.xsl" useImplicitFileset="false">
<mkdir dir="${package.output.dir}" />
<xslt destdir="${package.output.dir}" style="${package.xml.dir}/CreatePackager.xsl" useImplicitFileset="false">
<flattenmapper/>
<fileset dir="${package.xml.dir}">
<include name="${executable}.xml" />
@ -1057,11 +1127,11 @@
</fileset>
</xslt>
<ant antfile="${dist.dir}/packages/${executable}.xml" target="package" />
<ant antfile="${package.output.dir}/${executable}.xml" target="package" />
</target>
<target name="release" depends="package" description="release a build, putting each file in a location specified by the package">
<ant antfile="${dist.dir}/packages/${executable}.xml" target="release" />
<ant antfile="${package.output.dir}/${executable}.xml" target="release" />
</target>
<!-- Build a subset of picard with only those classes we need by completely abusing the packaging system -->
@ -1070,7 +1140,7 @@
<!-- Build out a classpath -->
<pathconvert property="required.picard.jars" pathsep=":">
<fileset dir="${basedir}">
<include name="staging" />
<include name="${staging.dir}" />
<include name="${lib.dir}/picard-*.*.*.jar" />
<include name="${lib.dir}/sam-*.jar" />
</fileset>
@ -1078,14 +1148,14 @@
<echo message="required.picard.jars=${required.picard.jars}" />
<!-- Stage picard-private -->
<delete dir="staging" />
<mkdir dir="staging" />
<unjar src="${picard.dist.dir}/picard-private.jar" dest="staging" overwrite="true" />
<delete dir="${staging.dir}" />
<mkdir dir="${staging.dir}" />
<unjar src="${picard.dist.dir}/picard-private.jar" dest="${staging.dir}" overwrite="true" />
<!-- Use the packaging system to extract parts of picard-private we need -->
<mkdir dir="${dist.dir}/packages" />
<xslt in="${package.xml.dir}/PicardPrivate.xml" out="${dist.dir}/packages/BuildPicardPrivate.xml" style="${package.xml.dir}/CreatePackager.xsl" />
<ant antfile="${dist.dir}/packages/BuildPicardPrivate.xml">
<mkdir dir="${package.output.dir}" />
<xslt in="${package.xml.dir}/PicardPrivate.xml" out="${package.output.dir}/BuildPicardPrivate.xml" style="${package.xml.dir}/CreatePackager.xsl" />
<ant antfile="${package.output.dir}/BuildPicardPrivate.xml">
<property name="additional.jars" value="${required.picard.jars}" />
</ant>
</target>
@ -1121,7 +1191,7 @@
<delete dir="${build.dir}"/>
<delete dir="${lib.dir}"/>
<delete dir="dump"/>
<delete dir="staging"/>
<delete dir="${staging.dir}"/>
<delete dir="${dist.dir}"/>
<delete dir="pipelinetests"/>
</target>

6
public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
View File

@ -379,8 +379,10 @@ class RodBindingArgumentTypeDescriptor extends ArgumentTypeDescriptor {
}
if ( tribbleType == null )
if ( ! file.canRead() | ! file.isFile() ) {
throw new UserException.BadArgumentValue(name, "Couldn't read file to determine type: " + file);
if ( ! file.exists() ) {
throw new UserException.CouldNotReadInputFile(file, "file does not exist");
} else if ( ! file.canRead() || ! file.isFile() ) {
throw new UserException.CouldNotReadInputFile(file, "file could not be read");
} else {
throw new UserException.CommandLineException(
String.format("No tribble type was provided on the command line and the type of the file could not be determined dynamically. " +

13
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
View File

@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.variantutils;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -133,7 +134,7 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
/**
* By default, this tool throws a UserException when it encounters a field without a value in some record. This
* is generally useful when you mistype -F CHROM, so that you get a friendly warning about CHRMO not being
* is generally useful when you mistype -F CHROM, so that you get a friendly warning about CHROM not being
* found before the tool runs through 40M 1000G records. However, in some cases you genuinely want to allow such
* fields (e.g., AC not being calculated for filtered records, if included). When provided, this argument
* will cause VariantsToTable to write out NA values for missing fields instead of throwing an error.
@ -294,6 +295,14 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
return x.toString();
}
});
getters.put("EVENTLENGTH", new Getter() { public String get(VariantContext vc) {
int maxLength = 0;
for ( final Allele a : vc.getAlternateAlleles() ) {
final int length = a.length() - vc.getReference().length();
if( Math.abs(length) > Math.abs(maxLength) ) { maxLength = length; }
}
return Integer.toString(maxLength);
}});
getters.put("QUAL", new Getter() { public String get(VariantContext vc) { return Double.toString(vc.getPhredScaledQual()); } });
getters.put("TRANSITION", new Getter() { public String get(VariantContext vc) {
if ( vc.isSNP() && vc.isBiallelic() )
@ -304,7 +313,7 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
getters.put("FILTER", new Getter() { public String get(VariantContext vc) {
return vc.isNotFiltered() ? "PASS" : Utils.join(",", vc.getFilters()); }
});
getters.put("ID", new Getter() { public String get(VariantContext vc) { return vc.hasID() ? vc.getID() : "."; } });
getters.put("HET", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHetCount()); } });
getters.put("HOM-REF", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHomRefCount()); } });
getters.put("HOM-VAR", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHomVarCount()); } });

19
public/java/src/org/broadinstitute/sting/utils/SimpleTimer.java
View File

@ -46,7 +46,7 @@ public class SimpleTimer {
* @return the name associated with this timer
*/
@Ensures("result != null")
public String getName() {
public synchronized String getName() {
return name;
}
@ -58,7 +58,7 @@ public class SimpleTimer {
*/
@Requires("running == false")
@Ensures({"result != null", "elapsed == 0l"})
public SimpleTimer start() {
public synchronized SimpleTimer start() {
elapsed = 0l;
restart();
return this;
@ -73,7 +73,7 @@ public class SimpleTimer {
*/
@Requires("running == false")
@Ensures("result != null")
public SimpleTimer restart() {
public synchronized SimpleTimer restart() {
running = true;
startTime = currentTime();
return this;
@ -82,14 +82,14 @@ public class SimpleTimer {
/**
* @return is this timer running?
*/
public boolean isRunning() {
public synchronized boolean isRunning() {
return running;
}
/**
* @return A convenience function to obtain the current time in milliseconds from this timer
*/
public long currentTime() {
public synchronized long currentTime() {
return System.currentTimeMillis();
}
@ -101,7 +101,7 @@ public class SimpleTimer {
*/
@Requires("running == true")
@Ensures({"result != null", "elapsed >= old(elapsed)", "running == false"})
public SimpleTimer stop() {
public synchronized SimpleTimer stop() {
running = false;
elapsed += currentTime() - startTime;
return this;
@ -116,12 +116,7 @@ public class SimpleTimer {
@Ensures({
"result >= (elapsed/1000.0)",
"result >= 0"})
public double getElapsedTime() {
public synchronized double getElapsedTime() {
return (running ? (currentTime() - startTime + elapsed) : elapsed) / 1000.0;
}
public void printElapsedTime(PrintStream out) {
out.printf("SimpleTimer %s: %.2f%n", name, getElapsedTime());
}
}

3
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
View File

@ -381,7 +381,8 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
}
}
attributes.put(VariantContext.ID_KEY, id);
if ( ! id.equals(VCFConstants.EMPTY_ID_FIELD) )
attributes.put(VariantContext.ID_KEY, id);
return attributes;
}

4
public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
View File

@ -111,6 +111,10 @@ public class UserException extends ReviewedStingException {
super(String.format("Couldn't read file because %s caused by %s", message, e.getMessage()));
}
public CouldNotReadInputFile(File file) {
super(String.format("Couldn't read file %s", file.getAbsolutePath()));
}
public CouldNotReadInputFile(File file, String message) {
super(String.format("Couldn't read file %s because %s", file.getAbsolutePath(), message));
}

2
public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
View File

@ -353,7 +353,7 @@ public class AlignmentUtils {
break;
case D:
case N:
refPos++;
refPos += elementLength;
break;
case M:
for ( int jjj = 0; jjj < elementLength; jjj++ ) {

2
public/java/test/org/broadinstitute/sting/MD5DB.java
View File

@ -239,7 +239,7 @@ public class MD5DB {
if ( ! expectedMD5.equals(filemd5sum) ) {
// we are going to fail for real in assertEquals (so we are counted by the testing framework).
// prepare ourselves for the comparison
System.out.printf("##### Test %s is going fail #####%n", name);
System.out.printf("##### Test %s is going to fail #####%n", name);
String pathToExpectedMD5File = getMD5FilePath(expectedMD5, "[No DB file found]");
String pathToFileMD5File = getMD5FilePath(filemd5sum, "[No DB file found]");
System.out.printf("##### Path to expected file (MD5=%s): %s%n", expectedMD5, pathToExpectedMD5File);

132
public/java/test/org/broadinstitute/sting/gatk/walkers/qc/TestVariantContextWalker.java 100755
View File

@ -0,0 +1,132 @@
/*
* Copyright (c) 2010 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.gatk.walkers.qc;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.ArgumentCollection;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
import org.broadinstitute.sting.gatk.walkers.Reference;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.gatk.walkers.Window;
import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.io.PrintStream;
import java.util.Arrays;
import java.util.EnumSet;
import java.util.List;
/**
* Test routine for new VariantContext object
*/
@Reference(window=@Window(start=-20,stop=1))
public class TestVariantContextWalker extends RodWalker<Integer, Integer> {
@Output
PrintStream out;
@ArgumentCollection
protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
@Argument(fullName="takeFirstOnly", doc="Only take the first second at a locus, as opposed to all", required=false)
boolean takeFirstOnly = false;
@Argument(fullName="onlyContextsOfType", doc="Only take variant contexts of this type", required=false)
VariantContext.Type onlyOfThisType = null;
@Argument(fullName="onlyContextsStartinAtCurrentPosition", doc="Only take variant contexts at actually start at the current position, excluding those at span to the current location but start earlier", required=false)
boolean onlyContextsStartinAtCurrentPosition = false;
@Argument(fullName="printPerLocus", doc="If true, we'll print the variant contexts, in addition to counts", required=false)
boolean printContexts = false;
@Argument(fullName="outputVCF", doc="If provided, we'll convert the first input context into a VCF", required=false)
VCFWriter writer = null;
private boolean wroteHeader = false;
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( ref == null )
return 0;
else {
EnumSet<VariantContext.Type> allowedTypes = onlyOfThisType == null ? null : EnumSet.of(onlyOfThisType);
int n = 0;
List<VariantContext> contexts;
if ( onlyContextsStartinAtCurrentPosition )
contexts = tracker.getValues(variantCollection.variants, context.getLocation());
else // ! onlyContextsStartinAtCurrentPosition
contexts = tracker.getValues(variantCollection.variants);
for ( VariantContext vc : contexts ) {
if ( allowedTypes == null || allowedTypes.contains(vc.getType()) ) {
// we need to trigger decoding of the genotype string to pass integration tests
vc.getGenotypes();
if ( writer != null && n == 0 ) {
if ( ! wroteHeader ) {
writer.writeHeader(VariantContextAdaptors.createVCFHeader(null, vc));
wroteHeader = true;
}
writer.add(vc);
}
n++;
if ( printContexts ) out.printf(" %s%n", vc);
if ( takeFirstOnly ) break;
}
}
if ( n > 0 && printContexts ) {
out.printf("%s => had %d variant context objects%n", context.getLocation(), n);
out.printf("---------------------------------------------%n");
}
return n;
}
}
public Integer reduceInit() {
return 0;
}
public Integer reduce(Integer point, Integer sum) {
return point + sum;
}
@Override
public void onTraversalDone(Integer result) {
// Double check traversal result to make count is the same.
// TODO: Is this check necessary?
out.println("[REDUCE RESULT] Traversal result is: " + result);
}
}

4
public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
View File

@ -89,7 +89,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@DataProvider(name = "trtestdata")
public Object[][] createTRTestData() {
new TRTest( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "2864f231fab7030377f3c8826796e48f" );
new TRTest( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "c164dd635721ba6df3f06dac1877c32d");
new TRTest( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "d04cf1f6df486e45226ebfbf93a188a5");
new TRTest( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "74314e5562c1a65547bb0edaacffe602" );
new TRTest( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "2a37c6001826bfabf87063b1dfcf594f" );
return TRTest.getTests(TRTest.class);
@ -200,7 +200,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testTableRecalibratorSolidIndelsRemoveRefBias() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "7d5edb75b176e4151de225f699719ee4" );
e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "2ad4c17ac3ed380071137e4e53a398a5" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();

21
public/java/test/org/broadinstitute/sting/utils/R/RScriptExecutorUnitTest.java
View File

@ -26,21 +26,12 @@ package org.broadinstitute.sting.utils.R;
import org.apache.commons.io.FileUtils;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.walkers.diffengine.DiffElement;
import org.broadinstitute.sting.gatk.walkers.diffengine.DiffEngine;
import org.broadinstitute.sting.gatk.walkers.diffengine.DiffNode;
import org.broadinstitute.sting.gatk.walkers.diffengine.Difference;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
/**
@ -49,7 +40,6 @@ import java.util.List;
public class RScriptExecutorUnitTest extends BaseTest {
final static String testrscript = "print(\"hello, world\")\n";
final static String publicRScript = "plot_Tranches.R";
final static String privateRScript = "variantCallQC.R";
// --------------------------------------------------------------------------------
//
@ -74,17 +64,6 @@ public class RScriptExecutorUnitTest extends BaseTest {
@Test
public void testPublic() { testOne(publicRScript, null, null, true); }
@Test
public void testPrivate() { testOne(privateRScript, null, null, true); }
// make sure we don't break finding something in private by adding another directory
@Test
public void testPrivateWithAdditionalPath1() { testOne(privateRScript, null, "dist", true); }
// make sure we don't break finding something in private by adding another directory
@Test
public void testPrivateWithAdditionalPath2() { testOne(privateRScript, null, "doesNotExist", true); }
@Test(expectedExceptions = UserException.class)
public void testNonExistantScriptException() { testOne("does_not_exist.R", null, null, true); }

10
public/packages/GATKEngine.xml
View File

@ -26,14 +26,10 @@
<package name="GATKEngine">
<executable name="GATKEngine">
<dependencies>
<!-- Core walkers -->
<package name="org.broadinstitute.sting.gatk.walkers.**" />
<!-- All non-oneoff GATK-specific RODs -->
<package name="org.broadinstitute.sting.utils.codecs.**" />
<!-- Filters -->
<package name="org.broadinstitute.sting.gatk.filters" />
<!-- Package everything in org.broadinstitute.sting -->
<package name="org.broadinstitute.sting.**" />
<!-- Tribble codecs -->
<package name="org.broad.tribble.*" />
<package name="org.broad.tribble.**" />
<!-- Workaround - depend on the logger impl required by JEXL -->
<package name="org.apache.commons.logging.impl" />
</dependencies>

2
public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala
View File

@ -36,8 +36,6 @@ class VcfGatherFunction extends CombineVariants with GatherFunction {
private lazy val originalGATK = this.originalFunction.asInstanceOf[CommandLineGATK]
override def freezeFieldValues {
this.memoryLimit = Some(1)
this.jarFile = this.originalGATK.jarFile
this.reference_sequence = this.originalGATK.reference_sequence
this.intervals = this.originalGATK.intervals