Added REFERENCE_BASES required annotation for performance

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1047 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java

@@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.traversals;
 import net.sf.samtools.SAMRecord;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.gatk.WalkerManager;
 import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
 import org.broadinstitute.sting.gatk.datasources.providers.ReadView;
 import org.broadinstitute.sting.gatk.datasources.providers.ReadReferenceView;
@@ -13,6 +14,7 @@ import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.Walker;
+import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.utils.GenomeLoc;
 
 import java.io.File;
@@ -103,7 +105,8 @@ public class TraverseReads extends TraversalEngine {
             throw new IllegalArgumentException("Unable to traverse reads; no read data is available.");
 
         ReadWalker<M, T> readWalker = (ReadWalker<M, T>) walker;
-
+        boolean needsReferenceBasesP = WalkerManager.isRequired(walker, DataSource.REFERENCE_BASES);
+        
         ReadView reads = new ReadView(dataProvider);
         ReadReferenceView reference = new ReadReferenceView(dataProvider);
 
@@ -116,7 +119,7 @@ public class TraverseReads extends TraversalEngine {
             // an array of characters that represent the reference
             char[] refSeq = null;
 
-            if (read.getReferenceIndex() >= 0) {
+            if (needsReferenceBasesP && read.getReferenceIndex() >= 0) {
                 // get the genome loc from the read
                 GenomeLoc site = new GenomeLoc(read);
 

java/src/org/broadinstitute/sting/gatk/walkers/CountReadsWalker.java

@@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.walkers;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.LocusContext;
 
+@Requires({DataSource.READS, DataSource.REFERENCE})
 public class CountReadsWalker extends ReadWalker<Integer, Integer> {
     public Integer map(char[] ref, SAMRecord read) {
         //System.out.println(read.format());

java/src/org/broadinstitute/sting/gatk/walkers/DataSource.java

@@ -17,5 +17,6 @@ package org.broadinstitute.sting.gatk.walkers;
  */
 public enum DataSource {
     READS,
-    REFERENCE
+    REFERENCE,
+    REFERENCE_BASES         // Do I actually need the reference bases passed to the walker?
 }

java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java

@@ -11,7 +11,7 @@ import org.broadinstitute.sting.gatk.LocusContext;
  * To change this template use File | Settings | File Templates.
  */
 @By(DataSource.READS)
-@Requires({DataSource.READS,DataSource.REFERENCE})
+@Requires({DataSource.READS,DataSource.REFERENCE, DataSource.REFERENCE_BASES})
 public abstract class LocusWalker<MapType, ReduceType> extends Walker<MapType, ReduceType> {
     // Do we actually want to operate on the context?
     public boolean filter(RefMetaDataTracker tracker, char ref, LocusContext context) {

java/src/org/broadinstitute/sting/gatk/walkers/LocusWindowWalker.java

@@ -12,7 +12,7 @@ import net.sf.samtools.SAMRecord;
  * Time: 2:52:28 PM
  * To change this template use File | Settings | File Templates.
  */
-@Requires({DataSource.READS,DataSource.REFERENCE})
+@Requires({DataSource.READS,DataSource.REFERENCE, DataSource.REFERENCE_BASES})
 public abstract class LocusWindowWalker<MapType, ReduceType> extends Walker<MapType, ReduceType> {
     // Do we actually want to operate on the context?
     public boolean filter(RefMetaDataTracker tracker, String ref, LocusContext context) {

java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java

@@ -43,6 +43,7 @@ import java.util.Random;
  * reads to a specified BAM file
  * The walker now also optionally filters reads based on command line options.
  */
+@Requires({DataSource.READS, DataSource.REFERENCE})
 public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
 
     /** an optional argument to dump the reads out to a BAM file */

java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java

@@ -9,7 +9,7 @@ import net.sf.samtools.SAMRecord;
  * Time: 2:52:28 PM
  * To change this template use File | Settings | File Templates.
  */
-@Requires(DataSource.READS)
+@Requires({DataSource.READS, DataSource.REFERENCE_BASES})
 public abstract class ReadWalker<MapType, ReduceType> extends Walker<MapType, ReduceType> {
     public boolean requiresOrderedReads() { return false; }
     

java/src/org/broadinstitute/sting/gatk/walkers/RefWalker.java

@@ -8,7 +8,7 @@ package org.broadinstitute.sting.gatk.walkers;
  * To change this template use File | Settings | File Templates.
  */
 @By(DataSource.REFERENCE)
-@Requires(DataSource.REFERENCE)
+@Requires({DataSource.REFERENCE, DataSource.REFERENCE_BASES})
 @Allows(DataSource.REFERENCE)
 public abstract class RefWalker<MapType, ReduceType> extends LocusWalker<MapType, ReduceType> {
 }