Resolving merge conflicts

public/java/src/org/broadinstitute/sting/gatk/report/GATKReportColumn.java

@@ -132,6 +132,7 @@ public class GATKReportColumn extends LinkedHashMap<Object, Object> {
     private static final Collection<String> RIGHT_ALIGN_STRINGS = Arrays.asList(
             "null",
             "NA",
+            "unknown",
             String.valueOf(Double.POSITIVE_INFINITY),
             String.valueOf(Double.NEGATIVE_INFINITY),
             String.valueOf(Double.NaN));
@@ -144,7 +145,7 @@ public class GATKReportColumn extends LinkedHashMap<Object, Object> {
      * @return true if the value is a right alignable
      */
     protected static boolean isRightAlign(String value) {
-        return value == null || RIGHT_ALIGN_STRINGS.contains(value) || NumberUtils.isNumber(value);
+        return value == null || RIGHT_ALIGN_STRINGS.contains(value) || NumberUtils.isNumber(value.trim());
     }
 
     /**
@@ -213,7 +214,7 @@ public class GATKReportColumn extends LinkedHashMap<Object, Object> {
     public Object put(Object key, Object value) {
         if (value != null) {
             String formatted = formatValue(value);
-            if (!formatted.equals("")) {
+            if (!formatted.equals("") && !formatted.equals("unknown")) {
                 updateMaxWidth(formatted);
                 updateFormat(formatted);
             }

public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java

@@ -61,6 +61,8 @@ public class GATKReportTable {
     private static final String COULD_NOT_READ_EMPTY_LINE = "Could not read the last empty line of this table -- ";
     private static final String OLD_GATK_TABLE_VERSION = "We no longer support older versions of the GATK Tables";
     
+    private static final String NUMBER_CONVERSION_EXCEPTION = "String is a number but is not a long or a double: ";
+
     public GATKReportTable(BufferedReader reader, GATKReportVersion version) {
         int counter = 0;
 
@@ -414,6 +416,8 @@ public class GATKReportTable {
         // This code below is bs. Why am do I have to conform to bad code
         // Below is some code to convert a string into its appropriate type.
         
+        // I second Roger's rant!
+
         // If we got a string but the column is not a String type
         Object newValue = null;
         if (value instanceof String && !column.getDataType().equals(GATKReportDataType.String)) {

public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java

@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.gatk.traversals;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.WalkerManager;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;

public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java

@@ -19,7 +19,7 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
  */
 @Analysis(description = "The overlap between eval and comp sites")
 public class CompOverlap extends VariantEvaluator implements StandardEval {
-    @DataPoint(description = "number of eval SNP sites", format = "%d")
+    @DataPoint(description = "number of eval variant sites", format = "%d")
     long nEvalVariants = 0;
 
     @DataPoint(description = "number of eval sites outside of comp sites", format = "%d")

public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java

@@ -26,18 +26,17 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
 import net.sf.picard.util.IntervalTree;
 import org.apache.log4j.Logger;
-import org.broad.tribble.Feature;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.annotator.SnpEff;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.interval.IntervalUtils;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
 
 /**
  * Stratifies the variants by whether they overlap an interval in the set provided on the command line.