Fixing problems with SAMQueryIterator and reads

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@263 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -125,8 +125,8 @@ public class ReferenceIterator implements Iterator<ReferenceIterator> {
         // we're somewhere on this contig
         if ( seekOffset < offset ) {
             // bad boy -- can't go backward safely
-            throw new IllegalArgumentException(String.format("Invalid seek to %s from %s, which is usually due to out of order reads%n",
+            throw new IllegalArgumentException(String.format("Invalid seek %s => %s, which is usually due to out of order reads%n",
-                    new GenomeLoc(currentContig.getName(), seekOffset), new GenomeLoc(currentContig.getName(), offset)));
+                    new GenomeLoc(currentContig.getName(), offset), new GenomeLoc(currentContig.getName(), seekOffset)));
         }
         else if ( seekOffset >= currentContig.length() ) {
             // bad boy -- can't go beyond the contig length
@@ -154,8 +154,8 @@ public class ReferenceIterator implements Iterator<ReferenceIterator> {
 
         if ( cmpContigs == -1 && false ) {  // todo: fixed
             // The contig we are looking for is before the currentContig -- it's an error
-            throw new IllegalArgumentException(String.format("Invalid seek to %s from %s, which is usually due to out of order reads%n",
+            throw new IllegalArgumentException(String.format("Invalid seek %s => %s, which is usually due to out of order reads%n",
-                    new GenomeLoc(currentContig.getName(), seekOffset), new GenomeLoc(currentContig.getName(), offset)));
+                    new GenomeLoc(currentContig.getName(), offset), new GenomeLoc(currentContig.getName(), seekOffset)));
         }
         else if ( cmpContigs == 1 ) {
             // we need to jump forward
@@ -163,8 +163,8 @@ public class ReferenceIterator implements Iterator<ReferenceIterator> {
 
             if ( ! refFile.seekToContig(seekContigName) ) { // ok, do the seek
                 // a false result indicates a failure, throw a somewhat cryptic call
-                throw new RuntimeIOException(String.format("Unexpected seek failure from %s from %s%n",
+                throw new RuntimeIOException(String.format("Unexpected seek failure from %s to %s%n",
-                        new GenomeLoc(currentContig.getName(), seekOffset), new GenomeLoc(currentContig.getName(), offset)));
+                        new GenomeLoc(currentContig.getName(), offset), new GenomeLoc(currentContig.getName(), seekOffset)));
             }
 
             readNextContig(); // since we haven't failed, we just read in the next contig (which is seekContigName)

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

@@ -75,6 +75,8 @@ public class SamQueryIterator implements Iterator<SAMRecord> {
                                                   (int)currentLoc.getStop() );
             if( recordIter.hasNext() )
                 break;
+            else
+                recordIter.close();
         }
     }
     

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

@@ -345,11 +345,11 @@ public abstract class TraversalEngine {
                 logger.fatal("Couldn't open file in sam file list: " + readsFile);
             }
         }
-        if (samReader.hasIndex()) {
+        //if (samReader.hasIndex()) {
-            return new SamQueryIterator(samReader, locs);
+        //    return new SamQueryIterator(samReader, locs);
-        } else {
+        //} else {
-            return samReader.iterator();
+        return samReader.iterator();
-        }
+        //}
     }
 
     protected Iterator<SAMRecord> WrapReadsIterator( final Iterator<SAMRecord> rawIterator, final boolean enableVerification ) {

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

@@ -5,6 +5,7 @@ import org.broadinstitute.sting.gatk.LocusContext;
 
 public class CountReadsWalker extends ReadWalker<Integer, Integer> {
     public Integer map(LocusContext context, SAMRecord read) {
+        //System.out.println(read.format());
         return 1;
     }