diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RodGeliText.java b/java/src/org/broadinstitute/sting/gatk/refdata/RodGeliText.java
index c2b452344..071cbd777 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/RodGeliText.java
+++ b/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;
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RodGenotypeChipAsGFF.java b/java/src/org/broadinstitute/sting/gatk/refdata/RodGenotypeChipAsGFF.java
index ca0664d30..ebe82a1d0 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/RodGenotypeChipAsGFF.java
+++ b/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;
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java b/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
index 76bba464d..b0c5fbc01 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
+++ b/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;
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java
index be4182b49..c2a4ce8bb 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java
+++ b/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;
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
index 90a13bf55..f9ea154ad 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
+++ b/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);
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java b/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
index 8db06aa9b..a20cc1ecb 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
+++ b/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;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/graphalign/GraphReferenceBuilder.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/graphalign/GraphReferenceBuilder.java
index 9d2308603..7afe6c837 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/graphalign/GraphReferenceBuilder.java
+++ b/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;
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/InvalidGenotypeException.java b/java/src/org/broadinstitute/sting/utils/genotype/InvalidGenotypeException.java
deleted file mode 100644
index 45c013d8e..000000000
--- a/java/src/org/broadinstitute/sting/utils/genotype/InvalidGenotypeException.java
+++ /dev/null
@@ -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);
- }
-}
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/Variation.java b/java/src/org/broadinstitute/sting/utils/genotype/Variation.java
deleted file mode 100644
index acde70d76..000000000
--- a/java/src/org/broadinstitute/sting/utils/genotype/Variation.java
+++ /dev/null
@@ -1,19 +0,0 @@
-package org.broadinstitute.sting.utils.genotype;
-
-import org.broadinstitute.sting.utils.GenomeLoc;
-
-import java.util.List;
-
-/**
- * @author aaron
- *
- * Interface Variant
- *
- * 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
- }
-}
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/tabular/TabularLFWriter.java b/java/src/org/broadinstitute/sting/utils/genotype/tabular/TabularLFWriter.java
deleted file mode 100644
index dc9d07afd..000000000
--- a/java/src/org/broadinstitute/sting/utils/genotype/tabular/TabularLFWriter.java
+++ /dev/null
@@ -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();
- }
- }
-}
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeEncoding.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeEncoding.java
index 61ed7a878..abcf969c6 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeEncoding.java
+++ b/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
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java
index be849f685..bf5090d1b 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java
+++ b/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() {
- if ( ! hasAlternateAllele() )
- return Variation.VARIANT_TYPE.REFERENCE;
-
+ public VCFGenotypeEncoding.TYPE getType() {
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
}
-
- 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");
+ return type;
}
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() {
diff --git a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFReaderUnitTest.java b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFReaderUnitTest.java
index e20919746..1097a120c 100644
--- a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFReaderUnitTest.java
+++ b/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;