Check for VCFConstants.MISSING_VALUE_v4 when retrieving INFO fields and consider such values as non-existent

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4603 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java

@@ -934,20 +934,43 @@ public class VariantContextUtils {
         return mergedAttribs;
     }
 
-    private static Boolean getBooleanAttribute(Map<String, Object> attribs, String attribName) {
+    public static Boolean getBooleanAttribute(Map<String, Object> attribs, String attribName) {
         Object val = attribs.get(attribName);
-        if (val == null)
+        if (val == null || val.equals(VCFConstants.MISSING_VALUE_v4))
             return null;
 
-        return new Boolean(val.toString());
+        try {
+            return new Boolean(val.toString());
+        }
+        catch (Exception e) {// IGNORE unparseable data
+            return null;
+        }
     }
 
-    private static String getStringAttribute(Map<String, Object> attribs, String attribName) {
+    public static String getStringAttribute(Map<String, Object> attribs, String attribName) {
         Object val = attribs.get(attribName);
-        if (val == null)
+        if (val == null || val.equals(VCFConstants.MISSING_VALUE_v4))
             return null;
 
-        return val.toString();
+        try {
+            return val.toString();
+        }
+        catch (Exception e) {// IGNORE unparseable data
+            return null;
+        }
+    }
+
+    public static Double getDoubleAttribute(Map<String, Object> attribs, String attribName) {
+        Object val = attribs.get(attribName);
+        if (val == null || val.equals(VCFConstants.MISSING_VALUE_v4))
+            return null;
+
+        try {
+            return new Double(val.toString());
+        }
+        catch (Exception e) {// IGNORE unparseable data
+            return null;
+        }
     }
 
     private static boolean mergeIntoMNPvalidationCheck(VariantContext vc1, VariantContext vc2) {

java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java

@@ -933,6 +933,8 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
      * @param result the number of reads and VariantContexts seen.
      */
     public void onTraversalDone(PhasingStats result) {
+        logger.debug("Entering onTraversalDone()");
+
         List<VariantContext> finalList = processQueue(result, true); // process all remaining data
         writeVcList(finalList);
         writer.close();
@@ -940,6 +942,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
         if (statsWriter != null)
             statsWriter.close();
 
+        System.out.println("Coverage over ALL samples:");
         System.out.println("Number of reads observed: " + result.getNumReads());
         System.out.println("Number of variant sites observed: " + result.getNumVarSites());
         System.out.println("Average coverage: " + ((double) result.getNumReads() / result.getNumVarSites()));

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypePhasingEvaluator.java

@@ -2,7 +2,9 @@ package org.broadinstitute.sting.gatk.walkers.varianteval;
 
 import org.broad.tribble.util.variantcontext.Genotype;
 import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broad.tribble.vcf.VCFConstants;
 import org.broadinstitute.sting.gatk.contexts.*;
+import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.*;
 import org.broadinstitute.sting.gatk.walkers.phasing.*;
 import org.broadinstitute.sting.utils.report.tags.Analysis;
@@ -205,11 +207,7 @@ public class GenotypePhasingEvaluator extends VariantEvaluator {
     }
 
     public static Double getPQ(Genotype gt) {
-        Object pq = gt.getAttributes().get(ReadBackedPhasingWalker.PQ_KEY);
+        return VariantContextUtils.getDoubleAttribute(gt.getAttributes(), ReadBackedPhasingWalker.PQ_KEY);
-        if (pq == null)
-            return null;
-
-        return new Double(pq.toString());
     }
 
     public boolean topMatchesTop(AllelePair b1, AllelePair b2) {