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Minor cleanup of TraverseReads

This commit is contained in:
Mark DePristo 2012-08-25 15:36:04 -04:00
parent 275a5e5439
commit e060b148e2
1 changed files with 23 additions and 29 deletions
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52
public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java
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@ -1,20 +1,3 @@
package org.broadinstitute.sting.gatk.traversals;
import net.sf.samtools.SAMRecord;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.ReadMetrics;
import org.broadinstitute.sting.gatk.WalkerManager;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.providers.ReadBasedReferenceOrderedView;
import org.broadinstitute.sting.gatk.datasources.providers.ReadReferenceView;
import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider;
import org.broadinstitute.sting.gatk.datasources.providers.ReadView;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
/*
* Copyright (c) 2009 The Broad Institute
*
@ -39,6 +22,19 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.traversals;
import net.sf.samtools.SAMRecord;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.providers.ReadBasedReferenceOrderedView;
import org.broadinstitute.sting.gatk.datasources.providers.ReadReferenceView;
import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider;
import org.broadinstitute.sting.gatk.datasources.providers.ReadView;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
/**
* @author aaron
@ -75,29 +71,27 @@ public class TraverseReads<M,T> extends TraversalEngine<M,T,ReadWalker<M,T>,Read
if( !dataProvider.hasReads() )
throw new IllegalArgumentException("Unable to traverse reads; no read data is available.");
ReadView reads = new ReadView(dataProvider);
ReadReferenceView reference = new ReadReferenceView(dataProvider);
final ReadView reads = new ReadView(dataProvider);
final ReadReferenceView reference = new ReadReferenceView(dataProvider);
// get the reference ordered data
ReadBasedReferenceOrderedView rodView = new ReadBasedReferenceOrderedView(dataProvider);
final ReadBasedReferenceOrderedView rodView = new ReadBasedReferenceOrderedView(dataProvider);
boolean done = walker.isDone();
// while we still have more reads
for (SAMRecord read : reads) {
for (final SAMRecord read : reads) {
if ( done ) break;
// ReferenceContext -- the reference bases covered by the read
ReferenceContext refContext = null;
// get the array of characters for the reference sequence, since we're a mapped read
if (!read.getReadUnmappedFlag() && dataProvider.hasReference())
refContext = reference.getReferenceContext(read);
// ReferenceContext -- the reference bases covered by the read
final ReferenceContext refContext = ! read.getReadUnmappedFlag() && dataProvider.hasReference()
? reference.getReferenceContext(read)
: null;
// update the number of reads we've seen
ReadMetrics readMetrics = dataProvider.getShard().getReadMetrics();
readMetrics.incrementNumIterations();
dataProvider.getShard().getReadMetrics().incrementNumIterations();
// if the read is mapped, create a metadata tracker
ReadMetaDataTracker tracker = (read.getReferenceIndex() >= 0) ? rodView.getReferenceOrderedDataForRead(read) : null;
final ReadMetaDataTracker tracker = read.getReferenceIndex() >= 0 ? rodView.getReferenceOrderedDataForRead(read) : null;
final boolean keepMeP = walker.filter(refContext, (GATKSAMRecord) read);
if (keepMeP) {