Merged bug fix from Stable into Unstable

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java

@@ -58,6 +58,13 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio
     // lacking a SnpEff version number in the VCF header:
     public static final String[] SUPPORTED_SNPEFF_VERSIONS = { "2.0.2" };
     public static final String SNPEFF_VCF_HEADER_VERSION_LINE_KEY = "SnpEffVersion";
+    public static final String SNPEFF_VCF_HEADER_COMMAND_LINE_KEY = "SnpEffCmd";
+
+    // When we write the SnpEff version number and command line to the output VCF, we change
+    // the key name slightly so that the output VCF won't be confused in the future for an
+    // output file produced by SnpEff directly:
+    public static final String OUTPUT_VCF_HEADER_VERSION_LINE_KEY = "Original" + SNPEFF_VCF_HEADER_VERSION_LINE_KEY;
+    public static final String OUTPUT_VCF_HEADER_COMMAND_LINE_KEY = "Original" + SNPEFF_VCF_HEADER_COMMAND_LINE_KEY;
 
     // SnpEff aggregates all effects (and effect metadata) together into a single INFO
     // field annotation with the key EFF:
@@ -165,10 +172,26 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio
         UNKNOWN
     }
 
-
+    public void initialize ( AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit, Set<VCFHeaderLine> headerLines ) {
-    public void initialize ( AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit ) {
+        // Make sure that we actually have a valid SnpEff rod binding (just in case the user specified -A SnpEff
+        // without providing a SnpEff rod via --snpEffFile):
         validateRodBinding(walker.getSnpEffRodBinding());
-        checkSnpEffVersion(walker, toolkit);
+        RodBinding<VariantContext> snpEffRodBinding = walker.getSnpEffRodBinding();
+
+        // Make sure that the SnpEff version number and command-line header lines are present in the VCF header of
+        // the SnpEff rod, and that the file was generated by a supported version of SnpEff:
+        VCFHeader snpEffVCFHeader = VCFUtils.getVCFHeadersFromRods(toolkit, Arrays.asList(snpEffRodBinding.getName())).get(snpEffRodBinding.getName());
+        VCFHeaderLine snpEffVersionLine = snpEffVCFHeader.getOtherHeaderLine(SNPEFF_VCF_HEADER_VERSION_LINE_KEY);
+        VCFHeaderLine snpEffCommandLine = snpEffVCFHeader.getOtherHeaderLine(SNPEFF_VCF_HEADER_COMMAND_LINE_KEY);
+
+        checkSnpEffVersion(snpEffVersionLine);
+        checkSnpEffCommandLine(snpEffCommandLine);
+
+        // If everything looks ok, add the SnpEff version number and command-line header lines to the
+        // header of the VCF output file, changing the key names so that our output file won't be
+        // mistaken in the future for a SnpEff output file:
+        headerLines.add(new VCFHeaderLine(OUTPUT_VCF_HEADER_VERSION_LINE_KEY, snpEffVersionLine.getValue()));
+        headerLines.add(new VCFHeaderLine(OUTPUT_VCF_HEADER_COMMAND_LINE_KEY, snpEffCommandLine.getValue()));
     }
 
     public Map<String, Object> annotate ( RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc ) {
@@ -204,12 +227,7 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio
         }
     }
 
-    private void checkSnpEffVersion ( AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit ) {
+    private void checkSnpEffVersion ( VCFHeaderLine snpEffVersionLine ) {
-        RodBinding<VariantContext> snpEffRodBinding = walker.getSnpEffRodBinding();
-
-        VCFHeader snpEffVCFHeader = VCFUtils.getVCFHeadersFromRods(toolkit, Arrays.asList(snpEffRodBinding.getName())).get(snpEffRodBinding.getName());
-        VCFHeaderLine snpEffVersionLine = snpEffVCFHeader.getOtherHeaderLine(SNPEFF_VCF_HEADER_VERSION_LINE_KEY);
-
         if ( snpEffVersionLine == null || snpEffVersionLine.getValue() == null || snpEffVersionLine.getValue().trim().length() == 0 ) {
             throw new UserException("Could not find a " + SNPEFF_VCF_HEADER_VERSION_LINE_KEY + " entry in the VCF header for the SnpEff " +
                                     "input file, and so could not verify that the file was generated by a supported version of SnpEff (" +
@@ -224,6 +242,14 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio
         }
     }
 
+    private void checkSnpEffCommandLine ( VCFHeaderLine snpEffCommandLine ) {
+        if ( snpEffCommandLine == null || snpEffCommandLine.getValue() == null || snpEffCommandLine.getValue().trim().length() == 0 ) {
+            throw new UserException("Could not find a " + SNPEFF_VCF_HEADER_COMMAND_LINE_KEY + " entry in the VCF header for the SnpEff " +
+                                    "input file, which should be added by all supported versions of SnpEff (" +
+                                    Arrays.toString(SUPPORTED_SNPEFF_VERSIONS) + ")");
+        }
+    }
+
     private boolean isSupportedSnpEffVersion ( String versionString ) {
         for ( String supportedVersion : SUPPORTED_SNPEFF_VERSIONS ) {
             if ( supportedVersion.equals(versionString) ) {
@@ -248,10 +274,13 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio
         List<SnpEffEffect> parsedEffects = new ArrayList<SnpEffEffect>();
 
         Object effectFieldValue = snpEffRecord.getAttribute(SNPEFF_INFO_FIELD_KEY);
-        List<String> individualEffects;
+        if ( effectFieldValue == null ) {
+            return parsedEffects;
+        }
 
         // The VCF codec stores multi-valued fields as a List<String>, and single-valued fields as a String.
         // We can have either in the case of SnpEff, since there may be one or more than one effect in this record.
+        List<String> individualEffects;
         if ( effectFieldValue instanceof List ) {
             individualEffects = (List<String>)effectFieldValue;
         }

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java

@@ -208,8 +208,6 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
             engine = new VariantAnnotatorEngine(annotationGroupsToUse, annotationsToUse, this, getToolkit());
         engine.initializeExpressions(expressionsToUse);
 
-        engine.invokeAnnotationInitializationMethods();
-
         // setup the header fields
         // note that if any of the definitions conflict with our new ones, then we want to overwrite the old ones
         Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
@@ -219,6 +217,8 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
                 hInfo.add(line);
         }
 
+        engine.invokeAnnotationInitializationMethods(hInfo);
+
         VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
         vcfWriter.writeHeader(vcfHeader);
 

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java

@@ -114,13 +114,13 @@ public class VariantAnnotatorEngine {
             dbAnnotations.put(rod, rod.getName());
     }
 
-    public void invokeAnnotationInitializationMethods() {
+    public void invokeAnnotationInitializationMethods( Set<VCFHeaderLine> headerLines ) {
         for ( VariantAnnotatorAnnotation annotation : requestedInfoAnnotations ) {
-            annotation.initialize(walker, toolkit);
+            annotation.initialize(walker, toolkit, headerLines);
         }
 
         for ( VariantAnnotatorAnnotation annotation : requestedGenotypeAnnotations ) {
-            annotation.initialize(walker, toolkit);
+            annotation.initialize(walker, toolkit, headerLines);
         }
     }
 

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java

@@ -25,9 +25,11 @@
 package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
 
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 
 import java.util.List;
+import java.util.Set;
 
 @DocumentedGATKFeature(enable = true, groupName = "VariantAnnotator annotations", summary = "VariantAnnotator annotations")
 public abstract class VariantAnnotatorAnnotation {
@@ -35,5 +37,5 @@ public abstract class VariantAnnotatorAnnotation {
     public abstract List<String> getKeyNames();
 
     // initialization method (optional for subclasses, and therefore non-abstract)
-    public void initialize ( AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit ) { }
+    public void initialize ( AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit, Set<VCFHeaderLine> headerLines ) { }
 }

public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java

@@ -134,7 +134,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
             validationDataLocation + "1kg_exomes_unfiltered.AFR.unfiltered.vcf --snpEffFile  " + validationDataLocation +
             "snpEff.AFR.unfiltered.vcf -L 1:1-1,500,000",
             1,
-            Arrays.asList("486fc6a5ca1819f5ab180d5d72b1ebc9")
+            Arrays.asList("ed9d1b37b0bd8b65ff9ce2688e0e102e")
         );
         executeTest("Testing SnpEff annotations", spec);
     }