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Added a new @PartitionBy for walkers to specify how to cut up their inputs. 

Now building all javadoc.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5428 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kshakir 2011-03-12 01:33:08 +00:00
parent 8ca3390ee0
commit 93de326066
8 changed files with 145 additions and 17 deletions
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26
build.xml
View File

@ -339,13 +339,13 @@
<pathelement location="${java.classes}" />
</path>
<javadoc doclet="org.broadinstitute.sting.utils.help.ResourceBundleExtractorDoclet"
docletpathref="doclet.classpath"
classpathref="external.dependencies"
additionalparam="-build-timestamp &quot;${build.timestamp}&quot; -version-suffix .${build.version} -out ${basedir}/${resource.path} -quiet">
<fileset refid="java.source.files"/>
<fileset refid="external.source.files"/>
</javadoc>
<javadoc doclet="org.broadinstitute.sting.utils.help.ResourceBundleExtractorDoclet"
docletpathref="doclet.classpath"
classpathref="external.dependencies"
additionalparam="-build-timestamp &quot;${build.timestamp}&quot; -version-suffix .${build.version} -out ${basedir}/${resource.path} -quiet">
<sourcepath path="${java.source.dir}"/>
<sourcepath path="${external.dir}"/>
</javadoc>
</target>
<target name="sting.compile" depends="gatk.compile, scala.compile" />
@ -710,12 +710,12 @@
</target>
<target name="javadoc" depends="init.buildall,resolve,queue-extensions.generate,init.scala.compile" description="generates javadoc">
<mkdir dir="javadoc"/>
<javadoc destdir="javadoc"
classpathref="external.dependencies">
<fileset refid="java.source.files"/>
<fileset refid="external.source.files"/>
</javadoc>
<mkdir dir="javadoc"/>
<javadoc destdir="javadoc"
classpathref="external.dependencies">
<sourcepath path="${java.source.dir}"/>
<sourcepath path="${external.dir}"/>
</javadoc>
<mkdir dir="scaladoc"/>
<scaladoc srcdir="" destdir="scaladoc" classpathref="scala.dependencies" deprecation="yes" unchecked="yes">
<src path="${scala.source.dir}"/>

1
java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java
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@ -19,6 +19,7 @@ import java.util.Arrays;
*/
@By(DataSource.READS)
@Requires({DataSource.READS,DataSource.REFERENCE, DataSource.REFERENCE_BASES})
@PartitionBy(PartitionType.Interval)
@ReadFilters({UnmappedReadFilter.class,NotPrimaryAlignmentReadFilter.class,DuplicateReadFilter.class,FailsVendorQualityCheckReadFilter.class})
public abstract class LocusWalker<MapType, ReduceType> extends Walker<MapType, ReduceType> {
// Do we actually want to operate on the context?

38
java/src/org/broadinstitute/sting/gatk/walkers/PartitionBy.java 100644
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@ -0,0 +1,38 @@
/*
* 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.gatk.walkers;
import java.lang.annotation.*;
/**
* Allows the walker to indicate how to partition data it wants to consume.
*/
@Documented
@Inherited
@Retention(RetentionPolicy.RUNTIME)
@Target(ElementType.TYPE)
public @interface PartitionBy {
PartitionType value();
}

54
java/src/org/broadinstitute/sting/gatk/walkers/PartitionType.java 100644
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@ -0,0 +1,54 @@
/*
* 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.gatk.walkers;
/**
* Defines the ways walkers inputs can be partitioned before
* being passed to multiple instances of the walker.
*/
public enum PartitionType {
/**
* Do not partition the walker inputs.
*/
None,
/**
* The walker inputs can be chunked down to the
* per-locus level.
*/
Locus,
/**
* The walker inputs should be processed as complete
* intervals defined -L or the reference contigs.
*/
Interval,
/**
* The walker inputs should always be processed as complete
* contigs, even if there are multiple intervals per contig.
*/
Contig
}

1
java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java
View File

@ -12,6 +12,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
* To change this template use File | Settings | File Templates.
*/
@Requires({DataSource.READS, DataSource.REFERENCE_BASES})
@PartitionBy(PartitionType.Contig)
public abstract class ReadWalker<MapType, ReduceType> extends Walker<MapType, ReduceType> {
public boolean requiresOrderedReads() { return false; }

1
java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
View File

@ -42,6 +42,7 @@ import org.apache.log4j.Logger;
* To change this template use File | Settings | File Templates.
*/
@ReadFilters(MalformedReadFilter.class)
@PartitionBy(PartitionType.None)
@BAQMode(QualityMode = BAQ.QualityMode.OVERWRITE_QUALS, ApplicationTime = BAQ.ApplicationTime.ON_INPUT)
public abstract class Walker<MapType, ReduceType> {
final protected static Logger logger = Logger.getLogger(Walker.class);

10
java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
View File

@ -39,6 +39,8 @@ import org.broadinstitute.sting.gatk.io.stubs.OutputStreamArgumentTypeDescriptor
import org.broadinstitute.sting.gatk.io.stubs.SAMFileReaderArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.walkers.PartitionBy;
import org.broadinstitute.sting.gatk.walkers.PartitionType;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.classloader.JVMUtils;
@ -209,10 +211,10 @@ public class GATKExtensionsGenerator extends CommandLineProgram {
* @return The scatter type for the walker.
*/
private String getScatterClass(Class<? extends Walker> walkerType) {
if (ReadWalker.class.isAssignableFrom(walkerType))
return "ContigScatterFunction";
else
return "IntervalScatterFunction";
PartitionType partitionType = walkerType.getAnnotation(PartitionBy.class).value();
if (partitionType == PartitionType.None)
return null;
return partitionType.name() + "ScatterFunction";
}
/**

31
scala/src/org/broadinstitute/sting/queue/extensions/gatk/LocusScatterFunction.scala 100644
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@ -0,0 +1,31 @@
/*
* 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.queue.extensions.gatk
/**
* For now returns an IntervalScatterFunction.
* TODO: A scatter function that divides down to the locus level.
*/
class LocusScatterFunction extends IntervalScatterFunction {}