Support for reseting the system; Cleanup later

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@174 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByHanger.java

@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.gatk.iterators;
 
 import net.sf.samtools.util.CloseableIterator;
+import net.sf.samtools.util.RuntimeIOException;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.AlignmentBlock;
 import org.broadinstitute.sting.utils.*;
@@ -29,13 +30,14 @@ public class LocusIteratorByHanger extends LocusIterator {
     private RefHanger<Integer> offsetHanger = new RefHanger<Integer>();
     final int INCREMENT_SIZE = 100;
     final boolean DEBUG = false;
+    boolean justCleared = false;
 
     // -----------------------------------------------------------------------------------------------------------------
     //
     // constructors and other basic operations
     //
     // -----------------------------------------------------------------------------------------------------------------
-    public LocusIteratorByHanger(final CloseableIterator<SAMRecord> samIterator) {
+    public LocusIteratorByHanger(final Iterator<SAMRecord> samIterator) {
         this.it = new PushbackIterator<SAMRecord>(samIterator);
     }
 
@@ -67,12 +69,29 @@ public class LocusIteratorByHanger extends LocusIterator {
         }        
     }
 
+    public void clear() {
+        System.out.printf("clear() called%n");
+        readHanger.clear();
+        offsetHanger.clear();
+    }
+
     // -----------------------------------------------------------------------------------------------------------------
     //
     // next() routine and associated collection operations
     //
     // -----------------------------------------------------------------------------------------------------------------
     public LocusContext next() {
+//        if ( it.hasNext() && ! readHanger.isEmpty() ) {
+//            // todo: this needs to be deleted
+//            final SAMRecord read = it.peek();
+//            GenomeLoc readLoc = Utils.genomicLocationOf(read);
+//            System.out.printf("Comparing %s to %s%n", readLoc, readHanger.getLeftLoc());
+//            if ( readLoc.compareTo(readHanger.getLeftLoc()) == -1 ) {
+//                clear();
+//                return next();
+//            }
+//        }
+
         if ( ! currentPositionIsFullyCovered() )
             expandWindow(INCREMENT_SIZE);
 
@@ -90,6 +109,7 @@ public class LocusIteratorByHanger extends LocusIterator {
     protected void hangRead(final SAMRecord read) {
         GenomeLoc readLoc = new GenomeLoc(read.getReferenceName(), read.getAlignmentStart());
         //System.out.printf("Adding read %s at %d%n", read.getReadName(), read.getAlignmentStart());
+        
         /*
         for ( int i = 0; i < read.getReadLength(); i++ ) {
             GenomeLoc offset = new GenomeLoc(readLoc.getContig(), readLoc.getStart() + i);
@@ -149,6 +169,7 @@ public class LocusIteratorByHanger extends LocusIterator {
             }
             
             SAMRecord read = it.next();
+            justCleared = false;
 
             GenomeLoc readLoc = Utils.genomicLocationOf(read);
             if ( DEBUG ) {
@@ -171,6 +192,57 @@ public class LocusIteratorByHanger extends LocusIterator {
         }
     }
 
+//    private final void expandWindow(final int incrementSize) {
+//        if ( DEBUG ) {
+//            System.out.printf("entering expandWindow..., hasNext=%b%n", it.hasNext());
+//            printState();
+//        }
+//
+//        while ( it.hasNext() ) {
+//            if ( DEBUG ) {
+//                System.out.printf("Expanding window%n");
+//                printState();
+//            }
+//
+//            try {
+//                SAMRecord read = it.next();
+//                justCleared = false;
+//
+//                GenomeLoc readLoc = Utils.genomicLocationOf(read);
+//                if ( DEBUG ) {
+//                    System.out.printf("  Expanding window sizes %d with %d : left=%s, right=%s, readLoc = %s, cmp=%d%n",
+//                            readHanger.size(), incrementSize,
+//                            readHanger.hasHangers() ? readHanger.getLeftLoc() : "NA",
+//                            readHanger.hasHangers() ? readHanger.getRightLoc() : "NA",
+//                            readLoc,
+//                            readHanger.hasHangers() ? readLoc.compareTo(readHanger.getLeftLoc()) : -100);
+//                }
+//                //if ( readHanger.size() >= incrementSize ) {
+//                //if ( readHanger.hasHangers() && readLoc.compareTo(readHanger.getLeftLoc()) == 1) {
+//                if ( readHanger.hasHangers() && readLoc.distance(readHanger.getLeftLoc()) >= incrementSize ) {
+//                    // We've collected up enough reads
+//                    it.pushback(read);
+//                    break;
+//                }
+//                else
+//                    hangRead(read);
+//            }
+//            catch ( RuntimeIOException rio ) {
+//                System.out.printf("Clearing state...");
+//                // todo: good god, this is dangerous, we are reseting state because the reads are out of order
+//                if ( ! justCleared ) {
+//                    rio.printStackTrace();
+//                    justCleared = true;
+//                    clear();
+//                }
+//                it.next(); // throw away the offending read
+//                expandWindow(INCREMENT_SIZE);
+//                return;
+//            }
+//        }
+//    }
+
+
     public void remove() {
         throw new UnsupportedOperationException("Can not remove records from a SAM file via an iterator!");
     }