From 091229e4dbf99666668ce8214f360e6138994fdb Mon Sep 17 00:00:00 2001
From: Christopher Hartl <chartl@broadinstitute.org>
Date: Wed, 9 Nov 2011 11:03:29 -0500
Subject: [PATCH] MVLikelihoodRatio now checks if the family string is provided
 before attempting to instantiate. Also check that variant contexts have both
 genotypes and genotype likelihoods. Table codec now yells at users for not
 providing a HEADER with the table - parsing tables without a header line was
 causing the first line of the file to be eaten. Table feature now has a
 toString method.

These are minor bug fixes.
---
 .../sting/gatk/walkers/annotator/MVLikelihoodRatio.java   | 8 ++++----
 .../sting/utils/codecs/table/TableCodec.java              | 6 ++++++
 .../sting/utils/codecs/table/TableFeature.java            | 6 ++++++
 3 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
index e0a2329f8..8da64608f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
@@ -33,7 +33,7 @@ public class MVLikelihoodRatio extends InfoFieldAnnotation implements Experiment
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( mendelianViolation == null ) {
-            if ( walker instanceof VariantAnnotator ) {
+            if ( walker instanceof VariantAnnotator && ((VariantAnnotator) walker).familyStr != null) {
                 mendelianViolation = new MendelianViolation(((VariantAnnotator)walker).familyStr, ((VariantAnnotator)walker).minGenotypeQualityP );
             }
             else {
@@ -42,9 +42,9 @@ public class MVLikelihoodRatio extends InfoFieldAnnotation implements Experiment
         }
 
         Map<String,Object> toRet = new HashMap<String,Object>(1);
-        boolean hasAppropriateGenotypes = vc.hasGenotype(mendelianViolation.getSampleChild()) &&
-                vc.hasGenotype(mendelianViolation.getSampleDad()) &&
-                vc.hasGenotype(mendelianViolation.getSampleMom());
+        boolean hasAppropriateGenotypes = vc.hasGenotype(mendelianViolation.getSampleChild()) && vc.getGenotype(mendelianViolation.getSampleChild()).hasLikelihoods() &&
+                vc.hasGenotype(mendelianViolation.getSampleDad()) && vc.getGenotype(mendelianViolation.getSampleDad()).hasLikelihoods() &&
+                vc.hasGenotype(mendelianViolation.getSampleMom()) && vc.getGenotype(mendelianViolation.getSampleMom()).hasLikelihoods();
         if ( hasAppropriateGenotypes )
             toRet.put("MVLR",mendelianViolation.violationLikelihoodRatio(vc));
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java
index 1919ccbf0..fac926587 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java
@@ -86,7 +86,13 @@ public class TableCodec implements ReferenceDependentFeatureCodec {
     public Object readHeader(LineReader reader) {
         String line = "";
         try {
+            boolean isFirst = true;
             while ((line = reader.readLine()) != null) {
+                System.out.println(line);
+                if ( isFirst && ! line.startsWith(headerDelimiter) ) {
+                    throw new UserException.MalformedFile("TableCodec file does not have a header");
+                }
+                isFirst &= false;
                 if (line.startsWith(headerDelimiter)) {
                     if (header.size() > 0) throw new IllegalStateException("Input table file seems to have two header lines.  The second is = " + line);
                     String spl[] = line.split(delimiterRegex);
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableFeature.java b/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableFeature.java
index a85849f0b..4b5c51bd4 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableFeature.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableFeature.java
@@ -1,7 +1,9 @@
 package org.broadinstitute.sting.utils.codecs.table;
 
+
 import org.broad.tribble.Feature;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.Utils;
 
 import java.util.List;
 
@@ -44,6 +46,10 @@ public class TableFeature implements Feature {
         return values.get(columnPosition);
     }
 
+    public String toString() {
+        return String.format("%s\t%s",position.toString(), Utils.join("\t",values));
+    }
+
     public String get(String columnName) {
         int position = keys.indexOf(columnName);
         if (position < 0) throw new IllegalArgumentException("We don't have a column named " + columnName);