Merge remote-tracking branch 'remotes/khalid/rodRefactor' into rodRefactor

Conflicts:
	public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
	public/java/test/org/broadinstitute/sting/BaseTest.java

build.xml

@@ -168,7 +168,7 @@
     <target name="init.buildall">
         <!-- Set the properties needed to build everything -->
         <property name="gatk.target" value="private"/>
-<!--         <property name="scala.target" value="core"/> -->
+        <property name="scala.target" value="core"/>
     </target>
 
     <target name="git.describe">
@@ -977,11 +977,11 @@
             <sourcepath path="${java.public.source.dir}"/>
             <sourcepath path="${external.dir}"/>
         </javadoc>
-<!--         <javadoc destdir="javadoc" -->
+        <javadoc destdir="javadoc"
-<!--                  classpathref="external.dependencies"> -->
+                 classpathref="external.dependencies">
-<!--             <sourcepath path="${java.private.source.dir}"/> -->
+            <sourcepath path="${java.private.source.dir}"/>
-<!--             <exclude name="**" unless="include.private" /> -->
+            <exclude name="**" unless="include.private" />
-<!--         </javadoc>         -->
+        </javadoc>        
         <mkdir dir="scaladoc"/>
         <scaladoc srcdir="" destdir="scaladoc" classpathref="scala.dependencies" deprecation="yes" unchecked="yes">
             <src path="${scala.public.source.dir}"/>

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

@@ -28,6 +28,7 @@ package org.broadinstitute.sting.gatk.walkers;
 import org.broad.tribble.Feature;
 import org.broad.tribble.dbsnp.DbSNPFeature;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Input;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -71,7 +72,7 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
     @Argument(fullName="showIndelPileups",shortName="show_indels",doc="In addition to base pileups, generate pileups of extended indel events")
     public boolean SHOW_INDEL_PILEUPS = false;
 
-    @Argument(fullName="metadata",shortName="metadata",doc="Add these ROD bindings to the output Pileup", required=false)
+    @Input(fullName="metadata",shortName="metadata",doc="Add these ROD bindings to the output Pileup", required=false)
     public List<RodBinding<Feature>> rods = Collections.emptyList();
 
     public void initialize() {

public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java

@@ -78,7 +78,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
 
     @Argument(fullName="maskExtension", shortName="maskExtend", doc="How many bases beyond records from a provided 'mask' rod should variants be filtered; [default:0]", required=false)
     protected Integer MASK_EXTEND = 0;
-    @Argument(fullName="maskName", shortName="mask", doc="The text to put in the FILTER field if a 'mask' rod is provided and overlaps with a variant call; [default:'Mask']", required=false)
+    @Argument(fullName="maskName", shortName="maskName", doc="The text to put in the FILTER field if a 'mask' rod is provided and overlaps with a variant call; [default:'Mask']", required=false)
     protected String MASK_NAME = "Mask";
 
     @Argument(fullName="missingValuesInExpressionsShouldEvaluateAsFailing", doc="When evaluating the JEXL expressions, should missing values be considered failing the expression (by default they are considered passing)?", required=false)

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java

@@ -108,6 +108,12 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
     @Argument(fullName="keepOriginalAC", shortName="keepOriginalAC", doc="Don't include filtered loci.", required=false)
     private boolean KEEP_ORIGINAL_CHR_COUNTS = false;
 
+    @Argument(fullName="discordance", shortName =  "disc", doc="Output variants that were not called on a ROD comparison track", required=false)
+    private RodBinding<VariantContext> discordanceTrack = RodBinding.makeUnbound(VariantContext.class);
+
+    @Argument(fullName="concordance", shortName =  "conc", doc="Output variants that were also called on a ROD comparison track", required=false)
+    private RodBinding<VariantContext> concordanceTrack = RodBinding.makeUnbound(VariantContext.class);
+
     @Hidden
     @Argument(fullName="keepAFSpectrum", shortName="keepAF", doc="Don't include loci found to be non-variant after the subsetting procedure.", required=false)
     private boolean KEEP_AF_SPECTRUM = false;

public/java/test/org/broadinstitute/sting/BaseTest.java

@@ -64,7 +64,7 @@ public abstract class BaseTest {
     public static final String b37Refseq = refseqAnnotationLocation + "refGene-big-table-b37.txt";
 
     public static final String dbsnpDataLocation = GATKDataLocation;
-    public static final String b36dbSNP129 = dbsnpDataLocation + "dbsnp_129_b36.vcf";
+    public static final String b36dbSNP129 = dbsnpDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf";
     public static final String b37dbSNP132 = dbsnpDataLocation + "dbsnp_132_b37.vcf";
 
     public static final String hapmapDataLocation = comparisonDataLocation + "Validated/HapMap/3.3/";