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More cleanup -- pushing shared functions down into the traversal engine. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@639 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-05-08 14:12:45 +00:00
parent 7a9cfe1f75
commit 483a58627b
7 changed files with 38 additions and 10 deletions
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4
java/src/org/broadinstitute/sting/gatk/dataSources/providers/ReferenceProvider.java
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@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.dataSources.providers;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
import org.broadinstitute.sting.gatk.dataSources.shards.Shard;
import edu.mit.broad.picard.reference.ReferenceSequence;
import net.sf.samtools.util.StringUtil;
@ -16,7 +17,8 @@ public class ReferenceProvider {
private ReferenceSequence referenceSequence;
private GenomeLoc referenceInterval;
public ReferenceProvider( IndexedFastaSequenceFile sequenceFile, GenomeLoc position ) {
public ReferenceProvider( IndexedFastaSequenceFile sequenceFile, Shard shard ) {
GenomeLoc position = shard.getGenomeLoc();
this.referenceSequence = sequenceFile.getSubsequenceAt( position.getContig(),
position.getStart(),
position.getStop() );

2
java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
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@ -117,7 +117,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Reduce
throw new StingException("Unable to retrieve result", ex );
}
traversalEngine.printOnTraversalDone("loci", result);
traversalEngine.printOnTraversalDone(result);
walker.onTraversalDone(result);
}

7
java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
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@ -5,12 +5,10 @@ import org.broadinstitute.sting.gatk.dataSources.providers.ReferenceProvider;
import org.broadinstitute.sting.gatk.dataSources.shards.Shard;
import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategy;
import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.SAMDataSource;
import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.SimpleDataSourceLoadException;
import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
import org.broadinstitute.sting.gatk.traversals.TraverseByReads;
import org.broadinstitute.sting.gatk.traversals.TraverseLociByReference;
import org.broadinstitute.sting.gatk.traversals.TraverseReads;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
@ -61,7 +59,7 @@ public class LinearMicroScheduler extends MicroScheduler {
StingSAMIterator readShard = dataSource.seek(shard);
ReferenceProvider referenceProvider = new ReferenceProvider(reference, shard.getGenomeLoc());
ReferenceProvider referenceProvider = new ReferenceProvider(reference, shard);
LocusContextProvider locusProvider = new LocusContextProvider(readShard);
if (!isAReadWalker) {
@ -73,8 +71,7 @@ public class LinearMicroScheduler extends MicroScheduler {
readShard.close();
}
String type = (isAReadWalker) ? "read" : "loci";
traversalEngine.printOnTraversalDone(type, accumulator);
traversalEngine.printOnTraversalDone(accumulator);
walker.onTraversalDone(accumulator);
}

4
java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
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@ -53,12 +53,12 @@ public class ShardTraverser implements Callable {
}
public Object call() {
Object accumulator = ((LocusWalker<?,?>)walker).reduceInit();
Object accumulator = walker.reduceInit();
CloseableIterator<SAMRecord> readShard = null;
readShard = reads.seek( shard );
ReferenceProvider referenceProvider = new ReferenceProvider( reference, shard.getGenomeLoc() );
ReferenceProvider referenceProvider = new ReferenceProvider( reference, shard );
LocusContextProvider locusProvider = new LocusContextProvider( readShard );
OutputTracker outputTracker = GenomeAnalysisTK.Instance.getOutputTracker();

12
java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
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@ -280,6 +280,16 @@ public abstract class TraversalEngine {
}
}
/**
* A passthrough method so that subclasses can report which types of traversals they're using.
* TODO: Make this method abstract once all traversals support it.
* @param sum Result of the computation.
* @param <T> Type of the computation.
*/
public <T> void printOnTraversalDone( T sum ) {
throw new UnsupportedOperationException( "This method should be overridden." );
}
/**
* Called after a traversal to print out information about the traversal process
*
@ -287,7 +297,7 @@ public abstract class TraversalEngine {
* @param sum The reduce result of the traversal
* @param <T> ReduceType of the traversal
*/
public <T> void printOnTraversalDone(final String type, T sum) {
protected <T> void printOnTraversalDone(final String type, T sum) {
printProgress(true, type, null);
logger.info("Traversal reduce result is " + sum);
final long curTime = System.currentTimeMillis();

10
java/src/org/broadinstitute/sting/gatk/traversals/TraverseLociByReference.java
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@ -90,4 +90,14 @@ public class TraverseLociByReference extends TraversalEngine {
return sum;
}
/**
* Temporary override of printOnTraversalDone.
* TODO: Add some sort of TE.getName() function once all TraversalEngines are ported.
* @param sum Result of the computation.
* @param <T> Type of the result.
*/
public <T> void printOnTraversalDone( T sum ) {
printOnTraversalDone( "loci", sum );
}
}

9
java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java
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@ -119,4 +119,13 @@ public class TraverseReads extends TraversalEngine {
return sum;
}
/**
* Temporary override of printOnTraversalDone.
* TODO: Add some sort of TE.getName() function once all TraversalEngines are ported.
* @param sum Result of the computation.
* @param <T> Type of the result.
*/
public <T> void printOnTraversalDone( T sum ) {
printOnTraversalDone( "reads", sum );
}
}