Refactor LIBS into utils.locusiterator before refactoring

public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusShardDataProvider.java

@@ -29,7 +29,7 @@ import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.gatk.ReadProperties;
 import org.broadinstitute.sting.gatk.datasources.reads.Shard;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
-import org.broadinstitute.sting.gatk.iterators.LocusIterator;
+import org.broadinstitute.sting.utils.locusiterator.LocusIterator;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 

public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java

@@ -28,7 +28,7 @@ package org.broadinstitute.sting.gatk.datasources.providers;
 import org.broadinstitute.sting.gatk.downsampling.DownsampleType;
 import org.broadinstitute.sting.gatk.ReadProperties;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.iterators.LocusIterator;
+import org.broadinstitute.sting.utils.locusiterator.LocusIterator;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 

public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java

@@ -29,9 +29,9 @@ import net.sf.picard.util.PeekableIterator;
 import org.broadinstitute.sting.gatk.ReadProperties;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.datasources.reads.Shard;
-import org.broadinstitute.sting.gatk.iterators.LegacyLocusIteratorByState;
+import org.broadinstitute.sting.utils.locusiterator.LegacyLocusIteratorByState;
-import org.broadinstitute.sting.gatk.iterators.LocusIterator;
+import org.broadinstitute.sting.utils.locusiterator.LocusIterator;
-import org.broadinstitute.sting.gatk.iterators.LocusIteratorByState;
+import org.broadinstitute.sting.utils.locusiterator.LocusIteratorByState;
 import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;

public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIterator.java

@@ -1,56 +0,0 @@
-/*
-* Copyright (c) 2012 The Broad Institute
-* 
-* Permission is hereby granted, free of charge, to any person
-* obtaining a copy of this software and associated documentation
-* files (the "Software"), to deal in the Software without
-* restriction, including without limitation the rights to use,
-* copy, modify, merge, publish, distribute, sublicense, and/or sell
-* copies of the Software, and to permit persons to whom the
-* Software is furnished to do so, subject to the following
-* conditions:
-* 
-* The above copyright notice and this permission notice shall be
-* included in all copies or substantial portions of the Software.
-* 
-* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
-* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-*/
-
-package org.broadinstitute.sting.gatk.iterators;
-
-import net.sf.samtools.util.CloseableIterator;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-
-import java.util.Iterator;
-
-/**
- * Iterator that traverses a SAM File, accumulating information on a per-locus basis
- */
-public abstract class LocusIterator implements Iterable<AlignmentContext>, CloseableIterator<AlignmentContext> {
-    // -----------------------------------------------------------------------------------------------------------------
-    //
-    // constructors and other basic operations
-    //
-    // -----------------------------------------------------------------------------------------------------------------
-    public Iterator<AlignmentContext> iterator() {
-        return this;
-    }
-
-    public void close() {
-        //this.it.close();
-    }
-
-    public abstract boolean hasNext();
-    public abstract AlignmentContext next();
-
-    public void remove() {
-        throw new UnsupportedOperationException("Can not remove records from a SAM file via an iterator!");
-    }
-}

public/java/src/org/broadinstitute/sting/utils/locusiterator/LegacyLocusIteratorByState.java

@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.iterators;
+package org.broadinstitute.sting.utils.locusiterator;
 
 import net.sf.picard.util.PeekableIterator;
 import net.sf.samtools.Cigar;

public/java/src/org/broadinstitute/sting/utils/locusiterator/LocusIterator.java

@@ -0,0 +1,31 @@
+package org.broadinstitute.sting.utils.locusiterator;
+
+import net.sf.samtools.util.CloseableIterator;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+
+import java.util.Iterator;
+
+/**
+ * Iterator that traverses a SAM File, accumulating information on a per-locus basis
+ */
+public abstract class LocusIterator implements Iterable<AlignmentContext>, CloseableIterator<AlignmentContext> {
+    // -----------------------------------------------------------------------------------------------------------------
+    //
+    // constructors and other basic operations
+    //
+    // -----------------------------------------------------------------------------------------------------------------
+    public Iterator<AlignmentContext> iterator() {
+        return this;
+    }
+
+    public void close() {
+        //this.it.close();
+    }
+
+    public abstract boolean hasNext();
+    public abstract AlignmentContext next();
+
+    public void remove() {
+        throw new UnsupportedOperationException("Can not remove records from a SAM file via an iterator!");
+    }
+}

public/java/src/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByState.java

@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.iterators;
+package org.broadinstitute.sting.utils.locusiterator;
 
 import net.sf.picard.util.PeekableIterator;
 import net.sf.samtools.Cigar;

public/java/test/org/broadinstitute/sting/gatk/datasources/reads/DownsamplerBenchmark.java

@@ -36,7 +36,7 @@ import org.broadinstitute.sting.gatk.ReadProperties;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
 import org.broadinstitute.sting.gatk.filters.ReadFilter;
 import org.broadinstitute.sting.gatk.filters.UnmappedReadFilter;
-import org.broadinstitute.sting.gatk.iterators.LegacyLocusIteratorByState;
+import org.broadinstitute.sting.utils.locusiterator.LegacyLocusIteratorByState;
 import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
 import org.broadinstitute.sting.gatk.walkers.qc.CountLoci;
 import org.broadinstitute.sting.utils.GenomeLocParser;

public/java/test/org/broadinstitute/sting/utils/locusiterator/LegacyLocusIteratorByStateUnitTest.java

@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.iterators;
+package org.broadinstitute.sting.utils.locusiterator;
 
 import net.sf.samtools.*;
 import net.sf.samtools.util.CloseableIterator;
@@ -33,6 +33,7 @@ import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
 import org.broadinstitute.sting.gatk.filters.ReadFilter;
+import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
@@ -49,6 +50,31 @@ import java.util.Collections;
 import java.util.Iterator;
 import java.util.List;
 
+/*
+ * Copyright (c) 2012 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 /**
  * testing of the LEGACY version of LocusIteratorByState
  */

public/java/test/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByStateUnitTest.java

@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.sting.gatk.iterators;
+package org.broadinstitute.sting.utils.locusiterator;
 
 import net.sf.samtools.*;
 import net.sf.samtools.util.CloseableIterator;
@@ -34,9 +34,11 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
 import org.broadinstitute.sting.gatk.downsampling.DownsamplingMethod;
 import org.broadinstitute.sting.gatk.filters.ReadFilter;
+import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.locusiterator.LocusIteratorByState;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;