new enum htsjdk.variant.variantcontext.StructuralVariantType describing the SV types

src/main/java/htsjdk/variant/variantcontext/StructuralVariantType.java

@@ -0,0 +1,47 @@
+/*
+ * The MIT License
+ *
+ * Copyright (c) 2016 Pierre Lindenbaum @yokofakun Institut du Thorax - Nantes - France
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */
+
+package htsjdk.variant.variantcontext;
+
+/**
+ * Type of Structural Variant as defined in the VCF spec 4.2
+ *
+ */
+public enum StructuralVariantType {
+    /** Deletion relative to the reference */
+    DEL,
+    /** Insertion of novel sequence relative to the reference */
+    INS,
+    /** Region of elevated copy number relative to the reference */
+    DUP,
+    /** Inversion of reference sequence */
+    INV,
+    /** Copy number variable region */
+    CNV,
+    /** breakend structural variation. VCF Specification : <cite>An arbitrary rearrangement
+     *  event can be summarized as a set of novel adjacencies.
+     *  Each adjacency ties together two breakends.</cite>
+     */
+    BND
+}

src/main/java/htsjdk/variant/variantcontext/VariantContext.java

@@ -1732,4 +1732,13 @@ public int getAlleleIndex(final Allele allele) {
         if ( index == -1 ) throw new IllegalArgumentException("Allele " + targetAllele + " not in this VariantContex " + this);
         return GenotypeLikelihoods.getPLIndecesOfAlleles(0, index);
     }
+    
+    /** 
+     * Search for the INFO=SVTYPE and return the type of Structural Variant 
+     * @return the StructuralVariantType of null if there is no property SVTYPE 
+     * */
+    public StructuralVariantType getStructuralVariantType() {
+        final String svType = this.getAttributeAsString(VCFConstants.SVTYPE, null);
+        return svType == null ? null : StructuralVariantType.valueOf(svType);
+    }
 }

src/main/java/htsjdk/variant/vcf/VCFConstants.java

@@ -63,7 +63,10 @@
     public static final String SOMATIC_KEY = "SOMATIC";
     public static final String VALIDATED_KEY = "VALIDATED";
     public static final String THOUSAND_GENOMES_KEY = "1000G";
-
+    
+    // reserved INFO for structural variants
+    /** INFO Type of structural variant */
+    public static final String SVTYPE = "SVTYPE";    
 
     // separators
     public static final String FORMAT_FIELD_SEPARATOR = ":";

src/test/java/htsjdk/variant/variantcontext/VariantContextUnitTest.java

@@ -26,6 +26,9 @@
 package htsjdk.variant.variantcontext;
 
 
+import htsjdk.samtools.util.CloseableIterator;
+import htsjdk.samtools.util.CloserUtil;
+
 // the imports for unit testing.
 
 import htsjdk.samtools.util.TestUtil;
@@ -37,6 +40,8 @@
 import htsjdk.tribble.TribbleException;
 import htsjdk.variant.VariantBaseTest;
 import htsjdk.variant.vcf.VCFConstants;
+import htsjdk.variant.vcf.VCFFileReader;
+
 import org.testng.Assert;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.BeforeSuite;
@@ -1447,4 +1452,30 @@ public void testExtraStrictValidationFailure(final VariantContext vc, final Alle
         // extraStrictValidation throws exceptions if it fails, so no Asserts here...
         vc.extraStrictValidation(reportedReference, observedReference, rsIDs);
     }
+    
+    
+    @DataProvider(name = "structuralVariationsTestData")
+    public Object[][] getStructuralVariationsTestData() {
+        return new Object[][] {
+         {new File("src/test/resources/htsjdk/variant/structuralvariants.vcf")}
+        };
+    }
+    
+    @Test(dataProvider = "structuralVariationsTestData")
+    public void testExtractStructuralVariationsData(final File vcfFile) {
+        VCFFileReader reader = null;
+        CloseableIterator<VariantContext> iter = null;
+        try {
+            reader = new VCFFileReader(vcfFile , false );
+            iter = reader.iterator();
+            while(iter.hasNext()) {
+                final VariantContext ctx = iter.next();
+                final StructuralVariantType st = ctx.getStructuralVariantType();
+                Assert.assertNotNull(st);
+            }
+        } finally {
+            CloserUtil.close(iter);
+            CloserUtil.close(reader);
+        }
+    }
 }

src/test/resources/htsjdk/variant/structuralvariants.vcf

@@ -0,0 +1,22 @@
+##fileformat=VCFv4.2
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+##INFO=<ID=END_CHR,Number=A,Type=String,Description="End chromosome of the variant described in this record">
+##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
+##INFO=<ID=SVLEN,Number=A,Type=Integer,Description="Difference in length between REF and ALT alleles">
+##INFO=<ID=SVTYPE,Number=A,Type=String,Description="Type of structural variant">
+##INFO=<ID=STRAND_1,Number=1,Type=String,Description="Strand Orientation of SV Start">
+##INFO=<ID=STRAND_2,Number=1,Type=String,Description="Strand Orientation of SV End">
+##INFO=<ID=METHOD,Number=1,Type=String,Description="SV Caller used to predict">
+##INFO=<ID=DP,Number=1,Type=String,Description="combined depth across samples">
+##ALT=<ID=DEL,Description="Deletion">
+##ALT=<ID=DUP,Description="Duplication">
+##ALT=<ID=INS,Description="Insertion of novel sequence">
+##ALT=<ID=INV,Description="Inversion">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=AO,Number=1,Type=Integer,Description="Alternate Allele Observations">
+##contig=<ID=1,length=14640000>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE1
+1	20	.	N	<DUP>	1	.	IMPRECISE;SVTYPE=DUP;END=4641652;END_CHR=1;STRAND_1=-;STRAND_2=+;SVLEN=4641632;METHOD=LUMPY;DP=90	GT:AO	1/1:90
+1	33	.	N	<DUP>	1	.	IMPRECISE;SVTYPE=DUP;END=2640388;END_CHR=1;STRAND_1=-;STRAND_2=+;SVLEN=2640355;METHOD=LUMPY;DP=3	GT:AO	1/1:3
+1	70	.	N	<DEL>	1	.	IMPRECISE;SVTYPE=DEL;END=4641583;END_CHR=1;STRAND_1=+;STRAND_2=-;SVLEN=-4641513;METHOD=LUMPY;DP=1	GT:AO	1/1:1
+1	101	.	N	<INV>	1	.	IMPRECISE;SVTYPE=INV;END=1988714;END_CHR=1;STRAND_1=-;STRAND_2=-;SVLEN=1988613;METHOD=LUMPY;DP=2	GT:AO	1/1:2