removing the Variation interface.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3216 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/refdata/RodGeliText.java

@@ -29,7 +29,6 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.genotype.Variation;
 
 import java.io.IOException;
 import java.util.ArrayList;

java/src/org/broadinstitute/sting/gatk/refdata/RodGenotypeChipAsGFF.java

@@ -5,7 +5,6 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
-import org.broadinstitute.sting.utils.genotype.Variation;
 
 import java.util.*;
 import java.util.regex.MatchResult;

java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java

@@ -2,7 +2,6 @@ package org.broadinstitute.sting.gatk.refdata;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.genotype.Variation;
 import org.broadinstitute.sting.utils.genotype.vcf.*;
 
 import java.io.File;

java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java

@@ -2,7 +2,6 @@ package org.broadinstitute.sting.gatk.refdata;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.genotype.Variation;
 
 import java.util.Arrays;
 import java.util.List;

java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java

@@ -8,7 +8,6 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.genotype.CalledGenotype;
 import org.broadinstitute.sting.utils.genotype.LikelihoodObject;
-import org.broadinstitute.sting.utils.genotype.Variation;
 import org.broadinstitute.sting.utils.genotype.geli.GeliTextWriter;
 import org.broadinstitute.sting.utils.genotype.glf.GLFSingleCall;
 import org.broadinstitute.sting.utils.genotype.glf.GLFWriter;
@@ -187,7 +186,7 @@ public class VariantContextAdaptors {
                 for ( VCFGenotypeEncoding s : vcfG.getAlleles() ) {
                     Allele a = Allele.getMatchingAllele(alleles, s.getBases());
                     if ( a == null ) {
-                        if ( vcf.getType() == Variation.VARIANT_TYPE.INSERTION || vcf.getType() == Variation.VARIANT_TYPE.DELETION )
+                        if ( vcf.isIndel() )
                             genotypeAlleles.add(refAllele);
                         else
                             throw new StingException("Invalid VCF genotype allele " + s + " in VCF " + vcf);

java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java

@@ -2,7 +2,6 @@ package org.broadinstitute.sting.gatk.refdata;
 
 import net.sf.samtools.util.SequenceUtil;
 import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.genotype.Variation;
 
 import java.util.ArrayList;
 import java.util.Arrays;

java/src/org/broadinstitute/sting/playground/gatk/walkers/graphalign/GraphReferenceBuilder.java

@@ -32,7 +32,6 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.gatk.walkers.RefWalker;
 import org.broadinstitute.sting.gatk.walkers.Requires;
@@ -40,7 +39,6 @@ import org.broadinstitute.sting.gatk.walkers.WalkerName;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.utils.genotype.Variation;
 
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;

java/src/org/broadinstitute/sting/utils/genotype/InvalidGenotypeException.java

@@ -1,20 +0,0 @@
-package org.broadinstitute.sting.utils.genotype;
-
-
-/**
- * 
- * @author aaron 
- * 
- * Class GenotypeException
- *
- * This exception is thrown when a genotype call is passed in that cannot be processed, i.e. invalid.
- */
-public class InvalidGenotypeException extends Exception {
-    public InvalidGenotypeException(String msg) {
-        super(msg);
-    }
-
-    public InvalidGenotypeException(String message, Throwable throwable) {
-        super(message, throwable);
-    }
-}

java/src/org/broadinstitute/sting/utils/genotype/Variation.java

@@ -1,19 +0,0 @@
-package org.broadinstitute.sting.utils.genotype;
-
-import org.broadinstitute.sting.utils.GenomeLoc;
-
-import java.util.List;
-
-/**
- * @author aaron
- *         <p/>
- *         Interface Variant
- *         <p/>
- *         This class represents a variant
- */
-public interface Variation {
-    // the types of variants we currently allow
-    public enum VARIANT_TYPE {
-        SNP, INSERTION, DELETION, REFERENCE // though reference is not really a variant, we need to represent it
-    }
-}

java/src/org/broadinstitute/sting/utils/genotype/tabular/TabularLFWriter.java

@@ -1,101 +0,0 @@
-package org.broadinstitute.sting.utils.genotype.tabular;
-
-import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.genotype.*;
-import org.broadinstitute.sting.gatk.contexts.variantcontext.*;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.PrintStream;
-import java.util.Arrays;
-
-
-/**
- * 
- * @author aaron 
- * 
- * Class TabularLF
- *
- * the tabular likelihood format, as an implementation of the genotype interface
- */
-public class TabularLFWriter implements GenotypeWriter {
-    /**
-     * where to print the tabular genotype likelihood info to
-     */
-    public PrintStream outStream;
-
-    /**
-     * construct, writing to a specified file
-     * @param writeTo file to write to
-     */
-    public TabularLFWriter(File writeTo) {
-        try {
-            outStream = new PrintStream(writeTo);
-        } catch (FileNotFoundException e) {
-            throw new StingException("Unable to write to specified file: " + writeTo.getName());
-        }
-        // print the header out
-        outStream.println("location sample_name ref alt genotype qhat qstar lodVsRef lodVsNextBest depth bases");
-    }
-
-    /**
-     * Add a genotype, given a variant context
-     *
-     * @param vc  the variant context representing the call to add
-     */
-    public void addCall(VariantContext vc) {
-        if ( vc.getNSamples() != 1 )
-            throw new IllegalArgumentException("The tabular LF format does not support multi-sample or no-calls");
-
-        org.broadinstitute.sting.gatk.contexts.variantcontext.Genotype genotype = vc.getGenotypes().values().iterator().next();
-        if ( genotype.isNoCall() )
-            throw new IllegalArgumentException("The tabular LF format does not support no-calls");
-
-        ReadBackedPileup pileup;
-        double[] likelihoods;
-        if ( genotype instanceof CalledGenotype) {
-            pileup = ((CalledGenotype)genotype).getReadBackedPileup();
-            likelihoods = ((CalledGenotype)genotype).getLikelihoods();
-        } else {
-            pileup = (ReadBackedPileup)genotype.getAttribute(CalledGenotype.READBACKEDPILEUP_ATTRIBUTE_KEY);
-            likelihoods = (double[])genotype.getAttribute(CalledGenotype.LIKELIHOODS_ATTRIBUTE_KEY);
-        }
-
-        if ( likelihoods == null ) {
-            likelihoods = new double[10];
-            Arrays.fill(likelihoods, Double.MIN_VALUE);
-        }
-
-        int readDepth = pileup == null ? -1 : pileup.size();
-
-        double nextVrsBest = 0;
-        double nextVrsRef = 0;
-        char ref = vc.getReference().toString().charAt(0);
-
-
-        /**
-         * This output is not correct, but I don't we even use this format anymore.  If we do, someone
-         * should change this code
-          */
-        outStream.println(String.format("%s %s %c %s %s %f %f %f %f %d %s",
-	                                        vc.getLocation().toString(),
-											"NOT OUTPUTED",
-	                                        ref,
-	                                        genotype.getGenotypeString(),
-											genotype.getGenotypeString(),
-	                                        -1,
-	                                        -1,
-                                            nextVrsRef,
-                                            nextVrsBest,
-	                                        readDepth,
-											genotype.getGenotypeString()));
-    }
-
-    /** finish writing, closing any open files. */
-    public void close() {
-        if (this.outStream != null) {
-            outStream.close();
-        }
-    }
-}

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeEncoding.java

@@ -13,7 +13,8 @@ public class VCFGenotypeEncoding {
         SINGLE_BASE,
         INSERTION,
         DELETION,
-        UNCALLED
+        UNCALLED,
+        MIXED // this type is only valid in aggregate, not for a single VCFGenotypeEncoding
     }
 
     // our length (0 for SINGLE_BASE), our bases, and our type

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java

@@ -277,37 +277,21 @@ public class VCFRecord {
         return 0.0;
     }
     
-    public Variation.VARIANT_TYPE getType() {
+    public VCFGenotypeEncoding.TYPE getType() {
-        if ( ! hasAlternateAllele() )
-            return Variation.VARIANT_TYPE.REFERENCE;
-
         VCFGenotypeEncoding.TYPE type = mAlts.get(0).getType();
         for (int i = 1; i < mAlts.size(); i++) {
             if ( mAlts.get(i).getType() != type )
-                throw new IllegalStateException("The record contains multiple encoding types");
+                return VCFGenotypeEncoding.TYPE.MIXED;  // if we have more than one type, return mixed
         }
-
+        return type;
-        switch ( type ) {
-            case SINGLE_BASE:
-                return Variation.VARIANT_TYPE.SNP;
-            case UNCALLED:
-                // If there are no alt alleles, all of the genotypes are reference or no calls, so we're a reference site
-                return Variation.VARIANT_TYPE.REFERENCE;
-            case DELETION:
-                return Variation.VARIANT_TYPE.DELETION;
-            case INSERTION:
-                return Variation.VARIANT_TYPE.INSERTION;
-        }
-
-        throw new IllegalStateException("The record contains unknown genotype encodings");
     }
 
     public boolean isDeletion() {
-        return getType() == Variation.VARIANT_TYPE.DELETION;
+        return getType() == VCFGenotypeEncoding.TYPE.DELETION;
     }
 
     public boolean isInsertion() {
-        return getType() == Variation.VARIANT_TYPE.INSERTION;
+        return getType() == VCFGenotypeEncoding.TYPE.INSERTION;
     }
 
     public boolean isIndel() {
@@ -315,7 +299,7 @@ public class VCFRecord {
     }
 
     public boolean isSNP() {
-        return getType() == Variation.VARIANT_TYPE.SNP;
+        return getType() == VCFGenotypeEncoding.TYPE.SINGLE_BASE;
     }
 
     public boolean isNovel() {

java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFReaderUnitTest.java

@@ -15,7 +15,6 @@ import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.refdata.RodVCF;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.genotype.Variation;
 import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 import org.junit.Assert;
 import org.junit.BeforeClass;