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Added the ability to get a merged header in a LociByReference traversal 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@514 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-04-23 20:34:52 +00:00
parent 282f1d88b8
commit 3dc2afd7ab
4 changed files with 37 additions and 15 deletions
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1
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
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@ -486,4 +486,5 @@ public class GenomeAnalysisTK extends CommandLineProgram {
}
public SAMFileReader getSamReader() { return this.engine.getSamReader(); }
public TraversalEngine getEngine() { return this.engine; }
}

3
java/src/org/broadinstitute/sting/gatk/executive/MicroManager.java
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@ -119,6 +119,9 @@ public class MicroManager {
ReferenceProvider referenceProvider = new ReferenceProvider( refIter );
LocusContextProvider locusProvider = new LocusContextProvider( readShard );
// set the sam header of the traversal engine
traversalEngine.setSAMHeader(readShard.getMergedHeader());
System.err.println(traversalEngine.getSAMHeader().getSequenceDictionary().toString());
accumulator = traversalEngine.traverse( walker, shard, referenceProvider, locusProvider, accumulator );
readShard.close();
}

29
java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
View File

@ -75,6 +75,11 @@ public abstract class TraversalEngine {
protected boolean THREADED_IO = false;
protected int THREADED_IO_BUFFER_SIZE = 10000;
// the stored header
protected SAMFileHeader myHeader = null;
/**
* our log, which we want to capture anything from this class
*/
@ -168,6 +173,26 @@ public abstract class TraversalEngine {
//
// --------------------------------------------------------------------------------------------------------------
/**
* get the associated SAM header for our run
* @return the header if it's stored, null if not
*/
public SAMFileHeader getSAMHeader() {
return myHeader;
}
/**
* set's the SAM header for this traversal, which should
* be the merged header in the multiple BAM file case.
*
* @param myHeader the passed in header
*/
public void setSAMHeader(SAMFileHeader myHeader) {
this.myHeader = myHeader;
}
/**
* Parses the location string locStr and sets the traversal engine to only process
* regions specified by the location string. The string is of the form:
@ -417,7 +442,7 @@ public abstract class TraversalEngine {
public boolean shutdown() {
// todo: actually shutdown the resources
return true;
}
@ -462,7 +487,7 @@ public abstract class TraversalEngine {
public <M, T> T traverse(Walker<M, T> walker, ArrayList<GenomeLoc> locations) {
return null;
}
// --------------------------------------------------------------------------------------------------------------
//
// traversal by loci functions

19
java/src/org/broadinstitute/sting/playground/gatk/walkers/ListSampleIds.java
View File

@ -1,28 +1,21 @@
package org.broadinstitute.sting.playground.gatk.walkers;
import net.sf.samtools.*;
import org.broadinstitute.sting.gatk.*;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
import org.broadinstitute.sting.gatk.refdata.rodGFF;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMReadGroupRecord;
import org.broadinstitute.sting.gatk.GenomeAnalysisTK;
import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.playground.gatk.walkers.AlleleFrequencyWalker;
import org.broadinstitute.sting.playground.utils.AlleleFrequencyEstimate;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import java.util.*;
import java.util.List;
public class ListSampleIds extends LocusWalker<Boolean, Boolean>
{
public void initialize()
{
GenomeAnalysisTK toolkit = this.getToolkit();
SAMFileHeader header = toolkit.getSamReader().getFileHeader();
SAMFileHeader header = toolkit.getEngine().getSAMHeader();
List<SAMReadGroupRecord> read_groups = header.getReadGroups();
for (int i = 0; i < read_groups.size(); i++)