Added an integration test for the SnpEff annotation support, as well as some extra safety checks and comments.

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

@@ -27,8 +27,8 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.codecs.snpEff.SnpEffConstants;
 import org.broadinstitute.sting.utils.codecs.snpEff.SnpEffFeature;
@@ -38,9 +38,22 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.*;
 
-public class SnpEff extends InfoFieldAnnotation implements StandardAnnotation {
+/**
+ * A set of genomic annotations based on the output of the SnpEff variant effect predictor tool
+ * (http://snpeff.sourceforge.net/).
+ *
+ * For each variant, chooses one of the effects of highest biological impact from the SnpEff
+ * output file (which must be bound to an RMD track named "SnpEff"), and adds annotations
+ * on that effect.
+ *
+ * The possible biological effects and their associated impacts are defined in the class:
+ * org.broadinstitute.sting.utils.codecs.snpEff.SnpEffConstants
+ *
+ * @author David Roazen
+ */
+public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotation {
 
-    // SnpEff field keys:
+    // SnpEff annotation key names:
     public static final String GENE_ID_KEY = "GENE_ID";
     public static final String GENE_NAME_KEY = "GENE_NAME";
     public static final String TRANSCRIPT_ID_KEY = "TRANSCRIPT_ID";
@@ -55,11 +68,14 @@ public class SnpEff extends InfoFieldAnnotation implements StandardAnnotation {
     public static final String CODON_NUM_KEY = "CODON_NUM";
     public static final String CDS_SIZE_KEY = "CDS_SIZE";
 
+    // Name of the RMD track bound to the raw SnpEff-generated output file:
     public static final String RMD_TRACK_NAME = "SnpEff";
 
     public Map<String, Object> annotate ( RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc ) {
         List<Object> snpEffFeatures = tracker.getReferenceMetaData(RMD_TRACK_NAME);
 
+        // Add only annotations for one of the most biologically-significant effects as defined in
+        // the SnpEffConstants class:
         SnpEffFeature mostSignificantEffect = getMostSignificantEffect(snpEffFeatures);
         return generateAnnotations(mostSignificantEffect);
     }

public/java/src/org/broadinstitute/sting/utils/codecs/snpEff/SnpEffCodec.java

@@ -34,6 +34,40 @@ import static org.broadinstitute.sting.utils.codecs.snpEff.SnpEffConstants.Zygos
 
 import java.io.IOException;
 
+/**
+ * Codec for decoding the output format of the SnpEff variant effect predictor tool
+ * (http://snpeff.sourceforge.net/).
+ *
+ * This format has 23 tab-delimited fields:
+ *
+ * Chromosome
+ * Position
+ * Reference
+ * Change
+ * Change Type: {SNP, MNP, INS, DEL}
+ * Zygosity: {Hom, Het}
+ * Quality
+ * Coverage
+ * Warnings
+ * Gene ID
+ * Gene Name
+ * Bio Type
+ * Transcript ID
+ * Exon ID
+ * Exon Rank
+ * Effect
+ * Old/New Amino Acid
+ * Old/New Codon
+ * Codon Num
+ * CDS Size
+ * Codons Around
+ * Amino Acids Around
+ * Custom Interval ID
+ *
+ * We treat all except the Chromosome, Position, and Effect fields as optional.
+ *
+ * @author David Roazen
+ */
 public class SnpEffCodec implements FeatureCodec {
 
     public static final int EXPECTED_NUMBER_OF_FIELDS = 23;
@@ -64,9 +98,13 @@ public class SnpEffCodec implements FeatureCodec {
                                                         "AAs around",
                                                         "Custom_interval_ID"
                                                       };
+
+    // The "Chromo", "Position", and "Effect" fields are required to be non-empty in every SnpEff output line:
     public static final int[] REQUIRED_FIELDS = { 0, 1, 15 };
+
     public static final String NON_CODING_GENE_FLAG = "WITHIN_NON_CODING_GENE";
 
+
     public Feature decodeLoc ( String line ) {
         return decode(line);
     }
@@ -101,6 +139,11 @@ public class SnpEffCodec implements FeatureCodec {
             Integer exonRank = tokens[14].isEmpty() ? null : Integer.parseInt(tokens[14]);
 
             boolean isNonCodingGene = isNonCodingGene(tokens[15]);
+
+            // Split the effect field into three subfields if the WITHIN_NON_CODING_GENE flag is present,
+            // otherwise split it into two subfields. We need this limit to prevent the extra effect-related information
+            // in the final field (when present) from being inappropriately tokenized:
+
             int effectFieldTokenLimit = isNonCodingGene ? 3 : 2;
             String[] effectFieldTokens = tokens[15].split(EFFECT_FIELD_DELIMITER_PATTERN, effectFieldTokenLimit);
             EffectType effect = parseEffect(effectFieldTokens, isNonCodingGene);
@@ -150,6 +193,9 @@ public class SnpEffCodec implements FeatureCodec {
     private EffectType parseEffect ( String[] effectFieldTokens, boolean isNonCodingGene ) {
         String effectName = "";
 
+        // If there's a WITHIN_NON_CODING_GENE flag, the effect name will be in the second subfield,
+        // otherwise it will be in the first subfield:
+
         if ( effectFieldTokens.length > 1 && isNonCodingGene ) {
             effectName = effectFieldTokens[1].trim();
         }
@@ -161,6 +207,9 @@ public class SnpEffCodec implements FeatureCodec {
     }
 
     private String parseEffectExtraInformation ( String[] effectFieldTokens, boolean isNonCodingGene ) {
+
+        // The extra effect-related information, if present, will always be the last subfield:
+
         if ( (effectFieldTokens.length == 2 && ! isNonCodingGene) || effectFieldTokens.length == 3 ) {
             return effectFieldTokens[effectFieldTokens.length - 1].trim();
         }

public/java/src/org/broadinstitute/sting/utils/codecs/snpEff/SnpEffConstants.java

@@ -24,8 +24,14 @@
 
 package org.broadinstitute.sting.utils.codecs.snpEff;
 
+/**
+ * A set of constants associated with the SnpEff codec.
+ *
+ * @author David Roazen
+ */
 public class SnpEffConstants {
 
+    // Possible SnpEff biological effects and their associated impacts:
     public enum EffectType {
         START_GAINED                      (EffectImpact.HIGH),
         START_LOST                        (EffectImpact.HIGH),
@@ -93,6 +99,7 @@ public class SnpEffConstants {
         }
     }
 
+    // The kinds of variants supported by the SnpEff output format:
     public enum ChangeType {
         SNP,
         MNP,
@@ -100,6 +107,7 @@ public class SnpEffConstants {
         DEL
     }
 
+    // Possible zygosities of SnpEff variants:
     public enum Zygosity {
         Hom,
         Het

public/java/src/org/broadinstitute/sting/utils/codecs/snpEff/SnpEffFeature.java

@@ -26,15 +26,26 @@ package org.broadinstitute.sting.utils.codecs.snpEff;
 
 import org.broad.tribble.Feature;
 
+import java.util.NoSuchElementException;
+
 import static org.broadinstitute.sting.utils.codecs.snpEff.SnpEffConstants.EffectType;
 import static org.broadinstitute.sting.utils.codecs.snpEff.SnpEffConstants.EffectImpact;
 import static org.broadinstitute.sting.utils.codecs.snpEff.SnpEffConstants.ChangeType;
 import static org.broadinstitute.sting.utils.codecs.snpEff.SnpEffConstants.Zygosity;
 
+/**
+ * Feature returned by the SnpEff codec -- stores the parsed field values from a line of SnpEff output.
+ *
+ * Many fields are optional, and missing values are represented by nulls. You should always call the
+ * hasX() method before calling the corresponding getX() method. Required fields can never be null
+ * and do not have a hasX() method.
+ *
+ * @author David Roazen
+ */
 public class SnpEffFeature implements Feature {
 
-    private String contig;
+    private String contig;                   // REQUIRED FIELD
-    private long position;
+    private long position;                   // REQUIRED FIELD
     private String reference;
     private String change;
     private ChangeType changeType;
@@ -48,8 +59,8 @@ public class SnpEffFeature implements Feature {
     private String transcriptID;
     private String exonID;
     private Integer exonRank;
-    private boolean isNonCodingGene;
+    private boolean isNonCodingGene;         // REQUIRED FIELD
-    private EffectType effect;
+    private EffectType effect;               // REQUIRED FIELD
     private String effectExtraInformation;
     private String oldAndNewAA;
     private String oldAndNewCodon;
@@ -85,6 +96,10 @@ public class SnpEffFeature implements Feature {
                            String aasAround,
                            String customIntervalID ) {
 
+        if ( contig == null || effect == null ) {
+            throw new IllegalArgumentException("contig and effect cannot be null, as they are required fields");
+        }
+
         this.contig = contig;
         this.position = position;
         this.reference = reference;
@@ -113,6 +128,10 @@ public class SnpEffFeature implements Feature {
     }
 
     public boolean isHigherImpactThan ( SnpEffFeature other ) {
+
+        // If one effect is in a non-coding gene and the other is not, the effect NOT in the
+        // non-coding gene has higher impact:
+
         if ( ! isNonCodingGene() && other.isNonCodingGene() ) {
             return true;
         }
@@ -120,6 +139,9 @@ public class SnpEffFeature implements Feature {
             return false;
         }
 
+        // Otherwise, both effects are either in or not in a non-coding gene, so we compare the impacts
+        // of the effects themselves as defined in the SnpEffConstants class:
+
         return getEffectImpact().isHigherImpactThan(other.getEffectImpact());
     }
 
@@ -140,6 +162,7 @@ public class SnpEffFeature implements Feature {
     }
 
     public String getReference() {
+        if ( reference == null ) throw new NoSuchElementException("This feature has no reference field");
         return reference;
     }
 
@@ -148,6 +171,7 @@ public class SnpEffFeature implements Feature {
     }
 
     public String getChange() {
+        if ( change == null ) throw new NoSuchElementException("This feature has no change field");
         return change;
     }
 
@@ -156,6 +180,7 @@ public class SnpEffFeature implements Feature {
     }
 
     public ChangeType getChangeType() {
+        if ( changeType == null ) throw new NoSuchElementException("This feature has no changeType field");
         return changeType;
     }
 
@@ -164,6 +189,7 @@ public class SnpEffFeature implements Feature {
     }
 
     public Zygosity getZygosity() {
+        if ( zygosity == null ) throw new NoSuchElementException("This feature has no zygosity field");
         return zygosity;
     }
 
@@ -172,6 +198,7 @@ public class SnpEffFeature implements Feature {
     }
 
     public Double getQuality() {
+        if ( quality == null ) throw new NoSuchElementException("This feature has no quality field");
         return quality;
     }
 
@@ -180,6 +207,7 @@ public class SnpEffFeature implements Feature {
     }
 
     public Long getCoverage() {
+        if ( coverage == null ) throw new NoSuchElementException("This feature has no coverage field");
         return coverage;
     }
 
@@ -188,6 +216,7 @@ public class SnpEffFeature implements Feature {
     }
 
     public String getWarnings() {
+        if ( warnings == null ) throw new NoSuchElementException("This feature has no warnings field");
         return warnings;
     }
 
@@ -196,6 +225,7 @@ public class SnpEffFeature implements Feature {
     }
 
     public String getGeneID() {
+        if ( geneID == null ) throw new NoSuchElementException("This feature has no geneID field");
         return geneID;
     }
 
@@ -204,6 +234,7 @@ public class SnpEffFeature implements Feature {
     }
 
     public String getGeneName() {
+        if ( geneName == null ) throw new NoSuchElementException("This feature has no geneName field");
         return geneName;
     }
 
@@ -212,6 +243,7 @@ public class SnpEffFeature implements Feature {
     }
 
     public String getBioType() {
+        if ( bioType == null ) throw new NoSuchElementException("This feature has no bioType field");
         return bioType;
     }
 
@@ -220,6 +252,7 @@ public class SnpEffFeature implements Feature {
     }
 
     public String getTranscriptID() {
+        if ( transcriptID == null ) throw new NoSuchElementException("This feature has no transcriptID field");
         return transcriptID;
     }
 
@@ -228,6 +261,7 @@ public class SnpEffFeature implements Feature {
     }
 
     public String getExonID() {
+        if ( exonID == null ) throw new NoSuchElementException("This feature has no exonID field");
         return exonID;
     }
 
@@ -236,6 +270,7 @@ public class SnpEffFeature implements Feature {
     }
 
     public Integer getExonRank() {
+        if ( exonRank == null ) throw new NoSuchElementException("This feature has no exonRank field");
         return exonRank;
     }
 
@@ -256,6 +291,7 @@ public class SnpEffFeature implements Feature {
     }
 
     public String getEffectExtraInformation() {
+        if ( effectExtraInformation == null ) throw new NoSuchElementException("This feature has no effectExtraInformation field");
         return effectExtraInformation;
     }
 
@@ -264,6 +300,7 @@ public class SnpEffFeature implements Feature {
     }
 
     public String getOldAndNewAA() {
+        if ( oldAndNewAA == null ) throw new NoSuchElementException("This feature has no oldAndNewAA field");
         return oldAndNewAA;
     }
 
@@ -272,6 +309,7 @@ public class SnpEffFeature implements Feature {
     }
 
     public String getOldAndNewCodon() {
+        if ( oldAndNewCodon == null ) throw new NoSuchElementException("This feature has no oldAndNewCodon field");
         return oldAndNewCodon;
     }
 
@@ -280,6 +318,7 @@ public class SnpEffFeature implements Feature {
     }
 
     public Integer getCodonNum() {
+        if ( codonNum == null ) throw new NoSuchElementException("This feature has no codonNum field");
         return codonNum;
     }
 
@@ -288,6 +327,7 @@ public class SnpEffFeature implements Feature {
     }
 
     public Integer getCdsSize() {
+        if ( cdsSize == null ) throw new NoSuchElementException("This feature has no cdsSize field");
         return cdsSize;
     }
 
@@ -296,6 +336,7 @@ public class SnpEffFeature implements Feature {
     }
 
     public String getCodonsAround() {
+        if ( codonsAround == null ) throw new NoSuchElementException("This feature has no codonsAround field");
         return codonsAround;
     }
 
@@ -304,6 +345,7 @@ public class SnpEffFeature implements Feature {
     }
 
     public String getAasAround() {
+        if ( aasAround == null ) throw new NoSuchElementException("This feature has no aasAround field");
         return aasAround;
     }
 
@@ -312,6 +354,7 @@ public class SnpEffFeature implements Feature {
     }
 
     public String getCustomIntervalID() {
+        if ( customIntervalID == null ) throw new NoSuchElementException("This feature has no customIntervalID field");
         return customIntervalID;
     }
 

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

@@ -125,4 +125,15 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
             executeTest("Testing lookup vcf tabix vs. vcf tribble", spec);
         }
     }
+
+    @Test
+    public void testSnpEffAnnotations() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+            "-T VariantAnnotator -R " + b37KGReference + " -o %s -A SnpEff -B:variant,VCF " + validationDataLocation + "/1000G.exomes.vcf " +
+            "-B:SnpEff,SnpEff " + validationDataLocation + "/snpEff_1.9.6_1000G.exomes.vcf_hg37.61.out" + " -L 1",
+            1,
+            Arrays.asList("5fe3644744d3c084a179c3d204555333")
+        );
+        executeTest("Testing SnpEff annotations", spec);
+    }
 }