Better default partition types for walkers

-- Added PartitionType.READ, and associated ReadScatterFunction.  ReadScatterFunction is literally just ContigScatterFunction until someone wants to implement something better
-- LocusWalkers (and subclasses RodWalkers and RefWalkers) are by default PartitionType.LOCUS.

public/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java

@@ -17,7 +17,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
  */
 @By(DataSource.READS)
 @Requires({DataSource.READS,DataSource.REFERENCE, DataSource.REFERENCE_BASES})
-@PartitionBy(PartitionType.INTERVAL)
+@PartitionBy(PartitionType.LOCUS)
 @ReadFilters({UnmappedReadFilter.class,NotPrimaryAlignmentFilter.class,DuplicateReadFilter.class,FailsVendorQualityCheckFilter.class})
 public abstract class LocusWalker<MapType, ReduceType> extends Walker<MapType, ReduceType> {
     // Do we actually want to operate on the context?

public/java/src/org/broadinstitute/sting/gatk/walkers/PartitionType.java

@@ -34,6 +34,12 @@ public enum PartitionType {
      */
     NONE,
 
+    /**
+     * The walker inputs can be chunked down to individual
+     * reads.
+     */
+    READ,
+
     /**
      * The walker inputs can be chunked down to the
      * per-locus level.

public/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java

@@ -12,7 +12,7 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
  * To change this template use File | Settings | File Templates.
  */
 @Requires({DataSource.READS, DataSource.REFERENCE_BASES})
-@PartitionBy(PartitionType.CONTIG)
+@PartitionBy(PartitionType.READ)
 public abstract class ReadWalker<MapType, ReduceType> extends Walker<MapType, ReduceType> {
     public boolean requiresOrderedReads() { return false; }
     

public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/ContigScatterFunction.scala

@@ -44,3 +44,4 @@ class ContigScatterFunction extends GATKScatterFunction with InProcessFunction {
     IntervalUtils.scatterContigIntervals(gi.samFileHeader, gi.locs, this.scatterOutputFiles)
   }
 }
+

public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/ReadScatterFunction.scala

@@ -0,0 +1,56 @@
+/*
+ * Copyright (c) 2011, 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.queue.extensions.gatk
+
+/*
+ * Copyright (c) 2011, 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.
+ */
+
+/**
+ * Currently ReadScatterFunction only does ContigScattering, but it
+ * could in principle do something more aggressive.
+ */
+class ReadScatterFunction extends ContigScatterFunction { }
+