Cleanup. Move filtering functions closer to where they're used.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@767 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/dataSources/providers/LocusContextQueue.java

@@ -5,13 +5,14 @@ import org.broadinstitute.sting.gatk.Reads;
 import org.broadinstitute.sting.gatk.dataSources.shards.Shard;
 import org.broadinstitute.sting.gatk.iterators.LocusContextIteratorByHanger;
 import org.broadinstitute.sting.gatk.iterators.LocusContextIterator;
-import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
+import org.broadinstitute.sting.gatk.traversals.TraversalStatistics;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import net.sf.samtools.SAMRecord;
 
 import java.util.Iterator;
 
 import edu.mit.broad.picard.filter.FilteringIterator;
+import edu.mit.broad.picard.filter.SamRecordFilter;
 /**
  * User: hanna
  * Date: May 13, 2009
@@ -36,7 +37,7 @@ public abstract class LocusContextQueue {
     private LocusContextIterator loci;    
 
     public LocusContextQueue(ShardDataProvider provider) {
-        Iterator<SAMRecord> reads = new FilteringIterator(provider.getReadIterator(), new TraversalEngine.locusStreamFilterFunc());
+        Iterator<SAMRecord> reads = new FilteringIterator(provider.getReadIterator(), new LocusStreamFilterFunc());
         this.loci = new LocusContextIteratorByHanger(reads);
         this.sourceInfo = provider.getReadIterator().getSourceInfo();
         this.shard = provider.getShard();
@@ -75,4 +76,43 @@ public abstract class LocusContextQueue {
         return loci.hasNext();
     }
 
+    /**
+     * Class to filter out un-handle-able reads from the stream.  We currently are skipping
+     * unmapped reads, non-primary reads, unaligned reads, and duplicate reads.
+     */
+    private static class LocusStreamFilterFunc implements SamRecordFilter {
+        SAMRecord lastRead = null;
+        public boolean filterOut(SAMRecord rec) {
+            boolean result = false;
+            String why = "";
+            if (rec.getReadUnmappedFlag()) {
+                TraversalStatistics.nUnmappedReads++;
+                result = true;
+                why = "Unmapped";
+            } else if (rec.getNotPrimaryAlignmentFlag()) {
+                TraversalStatistics.nNotPrimary++;
+                result = true;
+                why = "Not Primary";
+            } else if (rec.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START) {
+                TraversalStatistics.nBadAlignments++;
+                result = true;
+                why = "No alignment start";
+            } else if (rec.getDuplicateReadFlag()) {
+                TraversalStatistics.nDuplicates++;
+                result = true;
+                why = "Duplicate reads";
+            }
+            else {
+                result = false;
+            }
+
+            if (result) {
+                TraversalStatistics.nSkippedReads++;
+                //System.out.printf("  [filter] %s => %b %s", rec.getReadName(), result, why);
+            } else {
+                TraversalStatistics.nReads++;
+            }
+            return result;
+        }
+    }
 }

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

@@ -546,53 +546,6 @@ public abstract class TraversalEngine {
         throw new UnsupportedOperationException( "This method is a required override for new traversal engines.  Please port your traversal engine to the new style." );
     }
 
-
-    // --------------------------------------------------------------------------------------------------------------
-    //
-    // traversal by loci functions
-    //
-    // --------------------------------------------------------------------------------------------------------------
-
-    /**
-     * Class to filter out un-handle-able reads from the stream.  We currently are skipping
-     * unmapped reads, non-primary reads, unaligned reads, and duplicate reads.
-     */
-    public static class locusStreamFilterFunc implements SamRecordFilter {
-        SAMRecord lastRead = null;
-        public boolean filterOut(SAMRecord rec) {
-            boolean result = false;
-            String why = "";
-            if (rec.getReadUnmappedFlag()) {
-                TraversalStatistics.nUnmappedReads++;
-                result = true;
-                why = "Unmapped";
-            } else if (rec.getNotPrimaryAlignmentFlag()) {
-                TraversalStatistics.nNotPrimary++;
-                result = true;
-                why = "Not Primary";
-            } else if (rec.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START) {
-                TraversalStatistics.nBadAlignments++;
-                result = true;
-                why = "No alignment start";
-            } else if (rec.getDuplicateReadFlag()) {
-                TraversalStatistics.nDuplicates++;
-                result = true;
-                why = "Duplicate reads";
-            }
-            else {
-                result = false;
-            }
-
-            if (result) {
-                TraversalStatistics.nSkippedReads++;
-                //System.out.printf("  [filter] %s => %b %s", rec.getReadName(), result, why);
-            } else {
-                TraversalStatistics.nReads++;
-            }
-            return result;
-        }
-    }
-
     public void verifySortOrder(final boolean requiresSortedOrder) {
         if (beSafeP && !SORT_ON_FLY && samReader.getFileHeader().getSortOrder() != SAMFileHeader.SortOrder.coordinate) {
             final String msg = "SAM file is not sorted in coordinate order (according to header) Walker type with given arguments requires a sorted file for correct processing";