diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java
index 4b5d9979f..7ff27daf3 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java
@@ -136,9 +136,8 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "forHardLeftAlignVariantsTest.vcf --no_cmdline_in_header -split",
1,
- Arrays.asList("534bea653d4a0e59e74f4107c1768558"));
+ Arrays.asList("1158324223c312e4767fcefe9dde2fe1"));
executeTest("test left alignment with hard multiple alleles", spec);
-
}
@Test
@@ -146,8 +145,34 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "forHardLeftAlignVariantsTest.vcf --dontTrimAlleles --no_cmdline_in_header -split",
1,
- Arrays.asList("189b8136ee62b54bf7b227e99c892440"));
+ Arrays.asList("923cb1d06e2d0d9a98cda8f8f637d108"));
executeTest("test left alignment with hard multiple alleles, don't trim", spec);
+ }
+ @Test
+ public void testLeftAlignmentWithMultialleliecGenotypes() {
+ WalkerTestSpec spec = new WalkerTestSpec(
+ "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "multiallele-gt.vcf --no_cmdline_in_header -split",
+ 1,
+ Arrays.asList("f7be485b0cc7b8db75b7139f31c0708d"));
+ executeTest("test left alignment of multiple alleles with genoptypes", spec);
+ }
+
+ @Test
+ public void testLeftAlignmentWithMultialleliecGenotypesHetNoRef() {
+ WalkerTestSpec spec = new WalkerTestSpec(
+ "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "multiallele-gt-het-noref.vcf --no_cmdline_in_header -split",
+ 1,
+ Arrays.asList("cd686641ab7fe491a0acc7ff07535192"));
+ executeTest("test left alignment of multiple alleles with genoptypes, including het-noref", spec);
+ }
+
+ @Test
+ public void testLeftAlignmentWithMultialleliecGenotypesKeepOriginalAC() {
+ WalkerTestSpec spec = new WalkerTestSpec(
+ "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "multiallele-gt.vcf --no_cmdline_in_header -split -keepOriginalAC",
+ 1,
+ Arrays.asList("5da4ca9705fbb63446c1d317f7b6cae0"));
+ executeTest("test left alignment of multiple alleles with genoptypes, keep original AC", spec);
}
}
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java
index 0ba7e1013..49aa15477 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java
@@ -44,6 +44,9 @@ import org.broadinstitute.gatk.engine.walkers.Window;
import org.broadinstitute.gatk.engine.SampleUtils;
import org.broadinstitute.gatk.utils.collections.Pair;
import org.broadinstitute.gatk.utils.help.HelpConstants;
+import org.broadinstitute.gatk.utils.variant.ChromosomeCountConstants;
+import org.broadinstitute.gatk.utils.variant.GATKVCFConstants;
+import org.broadinstitute.gatk.utils.variant.GATKVCFHeaderLines;
import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
import htsjdk.variant.vcf.VCFHeader;
import htsjdk.variant.vcf.VCFHeaderLine;
@@ -118,7 +121,7 @@ import java.util.*;
* --splitMultiallelics
*
*
- * Split multiallelics into biallics, left align but don't trim alleles
+ * Split multiallelics into biallics, left align but don't trim alleles, and store the original AC, AF, and AN values
*
* java -jar GenomeAnalysisTK.jar \
* -T LeftAlignAndTrimVariants \
@@ -127,6 +130,7 @@ import java.util.*;
* -o output.vcf \
* --splitMultiallelics \
* --dontTrimAlleles
+ * --keepOriginalAC
*
*
*/
@@ -153,6 +157,14 @@ public class LeftAlignAndTrimVariants extends RodWalker {
@Argument(fullName="splitMultiallelics", shortName="split", doc="Split multiallelic records and left-align individual alleles", required=false)
protected boolean splitMultiallelics = false;
+ /**
+ * When subsetting a callset, this tool recalculates the AC, AF, and AN values corresponding to the contents of the
+ * subset. If this flag is enabled, the original values of those annotations will be stored in new annotations called
+ * AC_Orig, AF_Orig, and AN_Orig.
+ */
+ @Argument(fullName="keepOriginalAC", shortName="keepOriginalAC", doc="Store the original AC, AF, and AN values after subsetting", required=false)
+ private boolean keepOriginalChrCounts = false;
+
@Output(doc="File to which variants should be written")
protected VariantContextWriter baseWriter = null;
@@ -165,11 +177,21 @@ public class LeftAlignAndTrimVariants extends RodWalker {
private int referenceWindowStop;
public void initialize() {
- String trackName = variantCollection.variants.getName();
- Set samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName));
- Map vcfHeaders = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName));
+ final String trackName = variantCollection.variants.getName();
+ final Set samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName));
+ final Map vcfHeaders = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName));
+
+ final Set headerLines = new HashSet<>();
+ headerLines.addAll(vcfHeaders.get(trackName).getMetaDataInSortedOrder()) ;
+ if ( splitMultiallelics )
+ headerLines.addAll(Arrays.asList(ChromosomeCountConstants.descriptions));
+
+ if (keepOriginalChrCounts) {
+ headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.ORIGINAL_AC_KEY));
+ headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.ORIGINAL_AF_KEY));
+ headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.ORIGINAL_AN_KEY));
+ }
- Set headerLines = vcfHeaders.get(trackName).getMetaDataInSortedOrder();
baseWriter.writeHeader(new VCFHeader(headerLines, samples));
writer = VariantContextWriterFactory.sortOnTheFly(baseWriter, MAX_INDEL_LENGTH);
@@ -187,7 +209,8 @@ public class LeftAlignAndTrimVariants extends RodWalker {
for ( final VariantContext vc : VCs ) {
// split first into biallelics, and optionally don't trim alleles to minimal representation
if (splitMultiallelics) {
- final List vcList = GATKVariantContextUtils.splitVariantContextToBiallelics(vc);
+ final List vcList = GATKVariantContextUtils.splitVariantContextToBiallelics(vc, false,
+ GATKVariantContextUtils.GenotypeAssignmentMethod.BEST_MATCH_TO_ORIGINAL, keepOriginalChrCounts);
for (final VariantContext biallelicVC: vcList) {
changedSites += trimAlignWrite(biallelicVC, ref, vcList.size());
}
@@ -237,10 +260,6 @@ public class LeftAlignAndTrimVariants extends RodWalker {
// align the VC
final Pair result = alignAndWrite(v, ref);
- // strip out PLs and AD if we've subsetted the alleles
- if ( numBiallelics > 1 )
- result.first = new VariantContextBuilder(result.first).genotypes(GATKVariantContextUtils.stripPLsAndAD(result.first.getGenotypes())).make();
-
// write out new VC
writer.add(result.first);
@@ -301,7 +320,6 @@ public class LeftAlignAndTrimVariants extends RodWalker {
if ( !newCigar.equals(originalCigar) && newCigar.numCigarElements() > 1 ) {
int difference = originalIndex - newCigar.getCigarElement(0).getLength();
VariantContext newVC = new VariantContextBuilder(vc).start(vc.getStart()-difference).stop(vc.getEnd()-difference).make();
- //System.out.println("Moving record from " + vc.getChr()+":"+vc.getStart() + " to " + vc.getChr()+":"+(vc.getStart()-difference));
final int indelIndex = originalIndex-difference;
final byte[] newBases = new byte[indelLength + 1];
@@ -323,7 +341,7 @@ public class LeftAlignAndTrimVariants extends RodWalker {
* @param ref Ref bases
* @param indexOfRef Index in ref where to create indel
* @param indelLength Indel length
- * @return
+ * @return Haplotype, containing the reference and the indel
*/
@Requires({"vc != null","ref != null", "indexOfRef +indelLength < ref.length", "vc.getNAlleles() == 2"})
@Ensures("result != null")
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java
index 520582a47..db964663a 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java
@@ -31,6 +31,8 @@ import htsjdk.tribble.TribbleException;
import htsjdk.tribble.util.popgen.HardyWeinbergCalculation;
import htsjdk.variant.variantcontext.*;
import htsjdk.variant.vcf.VCFConstants;
+import htsjdk.variant.vcf.VCFHeaderLineCount;
+import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.apache.commons.lang.ArrayUtils;
import org.apache.log4j.Logger;
import org.broadinstitute.gatk.utils.*;
@@ -558,6 +560,12 @@ public class GATKVariantContextUtils {
*/
SET_TO_NO_CALL,
+ /**
+ * set all of the genotype GT values to NO_CALL and remove annotations
+ */
+ SET_TO_NO_CALL_NO_ANNOTATIONS,
+
+
/**
* Use the subsetted PLs to greedily assigned genotypes
*/
@@ -589,7 +597,7 @@ public class GATKVariantContextUtils {
}
/**
- * subset the Variant Context to the specific set of alleles passed in (pruning the PLs appropriately)
+ * Subset the Variant Context to the specific set of alleles passed in (pruning the PLs appropriately)
*
* @param vc variant context with genotype likelihoods
* @param allelesToUse which alleles from the vc are okay to use; *** must be in the same relative order as those in the original VC ***
@@ -601,6 +609,7 @@ public class GATKVariantContextUtils {
final GenotypeAssignmentMethod assignGenotypes) {
if ( vc == null ) throw new IllegalArgumentException("the VariantContext cannot be null");
if ( allelesToUse == null ) throw new IllegalArgumentException("the alleles to use cannot be null");
+ if ( allelesToUse.isEmpty() ) throw new IllegalArgumentException("must have alleles to use");
if ( allelesToUse.get(0).isNonReference() ) throw new IllegalArgumentException("First allele must be the reference allele");
if ( allelesToUse.size() == 1 ) throw new IllegalArgumentException("Cannot subset to only 1 alt allele");
@@ -896,6 +905,10 @@ public class GATKVariantContextUtils {
final GenotypeAssignmentMethod assignmentMethod,
final double[] newLikelihoods,
final List allelesToUse) {
+ if ( originalGT == null ) throw new IllegalArgumentException("originalGT cannot be null");
+ if ( gb == null ) throw new IllegalArgumentException("gb cannot be null");
+ if ( allelesToUse.isEmpty() || allelesToUse == null ) throw new IllegalArgumentException("allelesToUse cannot be empty or null");
+
switch ( assignmentMethod ) {
case DO_NOT_ASSIGN_GENOTYPES:
break;
@@ -903,6 +916,13 @@ public class GATKVariantContextUtils {
gb.alleles(NO_CALL_ALLELES);
gb.noGQ();
break;
+ case SET_TO_NO_CALL_NO_ANNOTATIONS:
+ gb.alleles(NO_CALL_ALLELES);
+ gb.noGQ();
+ gb.noAD();
+ gb.noPL();
+ gb.noAttributes();
+ break;
case USE_PLS_TO_ASSIGN:
if ( newLikelihoods == null || likelihoodsAreUninformative(newLikelihoods) ) {
// if there is no mass on the (new) likelihoods, then just no-call the sample
@@ -918,12 +938,10 @@ public class GATKVariantContextUtils {
break;
case BEST_MATCH_TO_ORIGINAL:
final List best = new LinkedList<>();
- final Allele ref = allelesToUse.get(0); // WARNING -- should be checked in input argument
+ final Allele ref = allelesToUse.get(0);
for ( final Allele originalAllele : originalGT ) {
best.add(allelesToUse.contains(originalAllele) ? originalAllele : ref);
}
- gb.noGQ();
- gb.noPL();
gb.alleles(best);
break;
}
@@ -970,7 +988,7 @@ public class GATKVariantContextUtils {
/**
* Assign genotypes (GTs) to the samples in the Variant Context greedily based on the PLs
*
- * @param vc variant context with genotype likelihoods
+ * @param vc variant context with genotype likelihoods
* @return genotypes context
*/
public static GenotypesContext assignDiploidGenotypes(final VariantContext vc) {
@@ -999,7 +1017,6 @@ public class GATKVariantContextUtils {
* Split variant context into its biallelic components if there are more than 2 alleles
*
* For VC has A/B/C alleles, returns A/B and A/C contexts.
- * Genotypes are all no-calls now (it's not possible to fix them easily)
* Alleles are right trimmed to satisfy VCF conventions
*
* If vc is biallelic or non-variant it is just returned
@@ -1008,21 +1025,63 @@ public class GATKVariantContextUtils {
*
* @param vc a potentially multi-allelic variant context
* @param trimLeft if true, we will also left trim alleles, potentially moving the resulting vcs forward on the genome
+ * @param genotypeAssignmentMethod assignment strategy for the (subsetted) PLs
* @return a list of bi-allelic (or monomorphic) variant context
*/
- public static List splitVariantContextToBiallelics(final VariantContext vc, final boolean trimLeft, final GenotypeAssignmentMethod genotypeAssignmentMethod) {
+ public static List splitVariantContextToBiallelics(final VariantContext vc, final boolean trimLeft, final GenotypeAssignmentMethod genotypeAssignmentMethod){
+ return splitVariantContextToBiallelics(vc, trimLeft,genotypeAssignmentMethod, false);
+ }
+
+ /**
+ * Split variant context into its biallelic components if there are more than 2 alleles
+ *
+ * For VC has A/B/C alleles, returns A/B and A/C contexts.
+ * Alleles are right trimmed to satisfy VCF conventions
+ *
+ * If vc is biallelic or non-variant it is just returned
+ *
+ * Chromosome counts are updated (but they are by definition 0)
+ *
+ * @param vc a potentially multi-allelic variant context
+ * @param trimLeft if true, we will also left trim alleles, potentially moving the resulting vcs forward on the genome
+ * @param genotypeAssignmentMethod assignment strategy for the (subsetted) PLs
+ * @param keepOriginalChrCounts keep the orignal chromosome counts before subsetting
+ * @return a list of bi-allelic (or monomorphic) variant context
+ */
+ public static List splitVariantContextToBiallelics(final VariantContext vc, final boolean trimLeft, final GenotypeAssignmentMethod genotypeAssignmentMethod,
+ final boolean keepOriginalChrCounts) {
+ if ( vc == null ) throw new IllegalArgumentException("vc cannot be null");
+
if ( ! vc.isVariant() || vc.isBiallelic() )
// non variant or biallelics already satisfy the contract
return Collections.singletonList(vc);
else {
final List biallelics = new LinkedList<>();
+ // if any of the genotypes ar ehet-not-ref (i.e. 1/2), set all of them to no-call
+ final GenotypeAssignmentMethod genotypeAssignmentMethodUsed = hasHetNonRef(vc.getGenotypes()) ? GATKVariantContextUtils.GenotypeAssignmentMethod.SET_TO_NO_CALL_NO_ANNOTATIONS : genotypeAssignmentMethod;
+
for ( final Allele alt : vc.getAlternateAlleles() ) {
- VariantContextBuilder builder = new VariantContextBuilder(vc);
+ final VariantContextBuilder builder = new VariantContextBuilder(vc);
+
+ // make biallelic alleles
final List alleles = Arrays.asList(vc.getReference(), alt);
builder.alleles(alleles);
- builder.genotypes(subsetDiploidAlleles(vc, alleles, genotypeAssignmentMethod));
- VariantContextUtils.calculateChromosomeCounts(builder, true);
+
+ // since the VC has been subset, remove the invalid attributes
+ for ( final String key : vc.getAttributes().keySet() ) {
+ if ( !(key.equals(VCFConstants.ALLELE_COUNT_KEY) || key.equals(VCFConstants.ALLELE_FREQUENCY_KEY) || key.equals(VCFConstants.ALLELE_NUMBER_KEY)) ||
+ genotypeAssignmentMethodUsed == GATKVariantContextUtils.GenotypeAssignmentMethod.SET_TO_NO_CALL_NO_ANNOTATIONS ) {
+ builder.rmAttribute(key);
+ }
+ }
+
+ // subset INFO field annotations if available if genotype is called
+ if ( genotypeAssignmentMethodUsed != GATKVariantContextUtils.GenotypeAssignmentMethod.SET_TO_NO_CALL_NO_ANNOTATIONS &&
+ genotypeAssignmentMethodUsed != GATKVariantContextUtils.GenotypeAssignmentMethod.SET_TO_NO_CALL )
+ addInfoFiledAnnotations(vc, builder, alt, keepOriginalChrCounts);
+
+ builder.genotypes(subsetDiploidAlleles(vc, alleles, genotypeAssignmentMethodUsed));
final VariantContext trimmed = trimAlleles(builder.make(), trimLeft, true);
biallelics.add(trimmed);
}
@@ -1031,6 +1090,21 @@ public class GATKVariantContextUtils {
}
}
+ /**
+ * Check if any of the genotypes is heterozygous, non-reference (i.e. 1/2)
+ *
+ * @param genotypesContext genotype information
+ * @return true if any of the genotypes are heterozygous, non-reference, false otherwise
+ */
+ private static boolean hasHetNonRef(final GenotypesContext genotypesContext ){
+ for (final Genotype gt : genotypesContext ) {
+ if (gt.isHetNonRef())
+ return true;
+ }
+ return false;
+ }
+
+
public static Genotype removePLsAndAD(final Genotype g) {
return ( g.hasLikelihoods() || g.hasAD() ) ? new GenotypeBuilder(g).noPL().noAD().make() : g;
}
@@ -1336,7 +1410,7 @@ public class GATKVariantContextUtils {
*
* @param originalGs the original GenotypesContext
* @param originalVC the original VariantContext
- * @param allelesToUse the new (sub)set of alleles to use
+ * @param allelesToUse the new subset of alleles to use
* @return a new non-null GenotypesContext
*/
static private GenotypesContext fixDiploidGenotypesFromSubsettedAlleles(final GenotypesContext originalGs, final VariantContext originalVC, final List allelesToUse) {
@@ -2121,4 +2195,91 @@ public class GATKVariantContextUtils {
return -1;
}
+
+ /**
+ * Add the VCF INFO field annotations for the used alleles
+ *
+ * @param vc original variant context
+ * @param builder variant context builder with subset of original variant context's alleles
+ * @param altAllele alternate allele
+ * @param keepOriginalChrCounts keep the orignal chromosome counts before subsetting
+ * @return variant context builder with updated INFO field attribute values
+ */
+ private static void addInfoFiledAnnotations(final VariantContext vc, final VariantContextBuilder builder, final Allele altAllele,
+ final boolean keepOriginalChrCounts){
+
+ if (vc == null) throw new IllegalArgumentException("the variant context cannot be null");
+ if (builder == null) throw new IllegalArgumentException("the variant context builder cannot be null");
+ if (builder.getAlleles() == null) throw new IllegalArgumentException("the variant context builder alleles cannot be null");
+
+ final List alleles = builder.getAlleles();
+ if (alleles.size() < 2) throw new IllegalArgumentException("the variant context builder must contain at least 2 alleles");
+
+ // don't have to subset, the original vc has the same number and hence, the same alleles
+ boolean keepOriginal = ( vc.getAlleles().size() == builder.getAlleles().size() );
+
+ if ( keepOriginalChrCounts ) {
+ if (vc.hasAttribute(VCFConstants.ALLELE_COUNT_KEY))
+ builder.attribute(GATKVCFConstants.ORIGINAL_AC_KEY, keepOriginal ?
+ vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY) : getAltAlleleInfoFieldValue(VCFConstants.ALLELE_COUNT_KEY, vc, altAllele));
+ if (vc.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY))
+ builder.attribute(GATKVCFConstants.ORIGINAL_AF_KEY, keepOriginal ?
+ vc.getAttribute(VCFConstants.ALLELE_FREQUENCY_KEY) : getAltAlleleInfoFieldValue(VCFConstants.ALLELE_FREQUENCY_KEY, vc, altAllele));
+ if (vc.hasAttribute(VCFConstants.ALLELE_NUMBER_KEY)) {
+ builder.attribute(GATKVCFConstants.ORIGINAL_AN_KEY, vc.getAttribute(VCFConstants.ALLELE_NUMBER_KEY));
+ }
+ }
+
+ VariantContextUtils.calculateChromosomeCounts(builder, true);
+ }
+
+
+ /**
+ * Get the alternate allele INFO field value
+ *
+ * @param infoFieldName VCF INFO field name
+ * @param vc variant context
+ * @param altAllele the alternate allele
+ * @return alternate allele INFO field value
+ * @throws ReviewedGATKException if the alternate allele is part of the variant context
+ */
+ private static Object getAltAlleleInfoFieldValue(final String infoFieldName, final VariantContext vc, final Allele altAllele) {
+
+ //final String[] splitOriginalField = vc.getAttribute(infoFieldName).toString().split(VCFConstants.INFO_FIELD_ARRAY_SEPARATOR);
+ final Object[] splitOriginalField = getVAttributeValues(vc.getAttribute(infoFieldName));
+
+ // subset the field
+ final boolean[] alleleIndexesToUse = getAlleleIndexBitset(vc, Arrays.asList(altAllele));
+
+ // skip the first allele, which is the reference
+ for (int i = 1; i < alleleIndexesToUse.length; i++) {
+ if (alleleIndexesToUse[i] == true)
+ return splitOriginalField[i-1];
+ }
+
+ throw new ReviewedGATKException("Alternate allele " + altAllele.toString() + " not in Variant Context " + vc.toString());
+ }
+
+ /**
+ * Pulls out the appropriate values for the INFO field attribute
+ *
+ * @param attribute INFO field attribute
+ * @return tokenized attribute values
+ */
+ private static Object[] getVAttributeValues(final Object attribute) {
+
+ if (attribute == null) throw new IllegalArgumentException("the attribute cannot be null");
+
+ // break the original attributes into separate tokens
+ final Object[] tokens;
+ if ( attribute.getClass().isArray() )
+ tokens = (Object[])attribute;
+ else if ( List.class.isAssignableFrom(attribute.getClass()) )
+ tokens = ((List)attribute).toArray();
+ else
+ tokens = attribute.toString().split(VCFConstants.INFO_FIELD_ARRAY_SEPARATOR);
+
+ return tokens;
+ }
}
+