Added a constructor, took out a copy constructor, and changed some SAMBAM code.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@335 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMBAMDataSource.java

@@ -103,7 +103,7 @@ public class SAMBAMDataSource implements SimpleDataSource {
      * @return an iterator for that region
      */
     public MergingSamRecordIterator2 seek(GenomeLoc location) {
-        MergingSamRecordIterator2 iter = new MergingSamRecordIterator2(this.mergeIterator);
+        MergingSamRecordIterator2 iter =  null; // new MergingSamRecordIterator2(this.mergeIterator.getMergedHeader().);
         if (locusMode) {
             iter.query(location.getContig(), (int) location.getStart(), (int) location.getStop(), true);
         } else {

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

@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.gatk.iterators;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.FastaSequenceFile2;
 
 import java.util.Iterator;
 
@@ -30,7 +31,7 @@ import java.util.Iterator;
  * <p/>
  * This class is a decorator class from Reference Iterator (though it is constrained
  * by the fact that referenceIterator.seekForwardOffset explicitly returns a referenceIterator
- * for now
+ * for now).
  * <p/>
  * TODO: Fix the underlying iterator and this class to model a real decorator pattern
  */
@@ -51,6 +52,16 @@ public class BoundedReferenceIterator implements Iterator<ReferenceIterator> {
     }
 
 
+    /**
+     * Create a BoundedReferenceIterator from a fasta seq and a genome loc
+     * @param refFile the fasta file, see the ReferenceIterator constructor
+     * @param loc our genome location
+     */
+    public BoundedReferenceIterator(FastaSequenceFile2 refFile, GenomeLoc loc) {
+        this.referenceIterator = new ReferenceIterator(refFile);
+        this.mLoc = loc;
+    }
+
     /**
      * isSubRegion
      * <p/>

java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java

@@ -59,26 +59,6 @@ public class MergingSamRecordIterator2 implements Iterator<SAMRecord> {
         }
     }
 
-    /**
-     * Constructs a new merging iterator with the same set of readers and sort order as
-     * provided by the header merger parameter.
-     */
-    public MergingSamRecordIterator2(MergingSamRecordIterator2 iter) {
-        this.samHeaderMerger = iter.samHeaderMerger;
-        this.sortOrder = iter.sortOrder;
-        initializePQ();
-
-        final SAMRecordComparator comparator = getComparator();
-        for (final SAMFileReader reader : samHeaderMerger.getReaders()) {
-            if (this.sortOrder != SAMFileHeader.SortOrder.unsorted && reader.getFileHeader().getSortOrder() != this.sortOrder) {
-                throw new PicardException("Files are not compatible with sort order: " + this.sortOrder);
-            }
-
-            final ComparableSamRecordIterator iterator = new ComparableSamRecordIterator(reader, comparator);
-            addIfNotEmpty(iterator);
-        }
-    }
-
 
     protected void initializePQ() {
         this.pq = new PriorityQueue<ComparableSamRecordIterator>(samHeaderMerger.getReaders().size());