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Revving the Tribble jar where the DbsnpCodec class was renamed to OldDbsnpCodec. Updating GATK code accordingly.

This commit is contained in:
Eric Banks 2011-09-06 20:39:42 -04:00
parent 9559115ad5
commit da9c8ab386
5 changed files with 16 additions and 23 deletions
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24
public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
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@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.refdata;
import net.sf.samtools.util.SequenceUtil;
import org.broad.tribble.Feature;
import org.broad.tribble.annotation.Strand;
import org.broad.tribble.dbsnp.DbSNPFeature;
import org.broad.tribble.dbsnp.OldDbSNPFeature;
import org.broad.tribble.gelitext.GeliTextFeature;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.classloader.PluginManager;
@ -93,27 +93,27 @@ public class VariantContextAdaptors {
// --------------------------------------------------------------------------------------------------------------
private static class DBSnpAdaptor implements VCAdaptor {
private static boolean isSNP(DbSNPFeature feature) {
private static boolean isSNP(OldDbSNPFeature feature) {
return feature.getVariantType().contains("single") && feature.getLocationType().contains("exact");
}
private static boolean isMNP(DbSNPFeature feature) {
private static boolean isMNP(OldDbSNPFeature feature) {
return feature.getVariantType().contains("mnp") && feature.getLocationType().contains("range");
}
private static boolean isInsertion(DbSNPFeature feature) {
private static boolean isInsertion(OldDbSNPFeature feature) {
return feature.getVariantType().contains("insertion");
}
private static boolean isDeletion(DbSNPFeature feature) {
private static boolean isDeletion(OldDbSNPFeature feature) {
return feature.getVariantType().contains("deletion");
}
private static boolean isIndel(DbSNPFeature feature) {
private static boolean isIndel(OldDbSNPFeature feature) {
return isInsertion(feature) || isDeletion(feature) || isComplexIndel(feature);
}
public static boolean isComplexIndel(DbSNPFeature feature) {
public static boolean isComplexIndel(OldDbSNPFeature feature) {
return feature.getVariantType().contains("in-del");
}
@ -125,7 +125,7 @@ public class VariantContextAdaptors {
*
* @return an alternate allele list
*/
public static List<String> getAlternateAlleleList(DbSNPFeature feature) {
public static List<String> getAlternateAlleleList(OldDbSNPFeature feature) {
List<String> ret = new ArrayList<String>();
for (String allele : getAlleleList(feature))
if (!allele.equals(String.valueOf(feature.getNCBIRefBase()))) ret.add(allele);
@ -139,7 +139,7 @@ public class VariantContextAdaptors {
*
* @return an alternate allele list
*/
public static List<String> getAlleleList(DbSNPFeature feature) {
public static List<String> getAlleleList(OldDbSNPFeature feature) {
List<String> alleleList = new ArrayList<String>();
// add ref first
if ( feature.getStrand() == Strand.POSITIVE )
@ -156,14 +156,14 @@ public class VariantContextAdaptors {
/**
* Converts non-VCF formatted dbSNP records to VariantContext.
* @return DbSNPFeature.
* @return OldDbSNPFeature.
*/
@Override
public Class<? extends Feature> getAdaptableFeatureType() { return DbSNPFeature.class; }
public Class<? extends Feature> getAdaptableFeatureType() { return OldDbSNPFeature.class; }
@Override
public VariantContext convert(String name, Object input, ReferenceContext ref) {
DbSNPFeature dbsnp = (DbSNPFeature)input;
OldDbSNPFeature dbsnp = (OldDbSNPFeature)input;
if ( ! Allele.acceptableAlleleBases(dbsnp.getNCBIRefBase()) )
return null;
Allele refAllele = Allele.create(dbsnp.getNCBIRefBase(), true);

11
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
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@ -26,7 +26,6 @@
package org.broadinstitute.sting.gatk.walkers.variantutils;
import org.broad.tribble.TribbleException;
import org.broad.tribble.dbsnp.DbSNPFeature;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
@ -41,7 +40,6 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.io.File;
import java.util.Collection;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
@ -168,14 +166,9 @@ public class ValidateVariants extends RodWalker<Integer, Integer> {
// get the RS IDs
Set<String> rsIDs = null;
if ( tracker.hasValues(dbsnp.dbsnp) ) {
List<VariantContext> dbsnpList = tracker.getValues(dbsnp.dbsnp, ref.getLocus());
rsIDs = new HashSet<String>();
for ( Object d : dbsnpList ) {
if (d instanceof DbSNPFeature )
rsIDs.add(((DbSNPFeature)d).getRsID());
else if (d instanceof VariantContext )
rsIDs.add(((VariantContext)d).getID());
}
for ( VariantContext rsID : tracker.getValues(dbsnp.dbsnp, ref.getLocus()) )
rsIDs.add(rsID.getID());
}
try {

2
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java
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@ -23,7 +23,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
" --variant:dbsnp " + GATKDataLocation + "Comparisons/Validated/dbSNP/dbsnp_129_b36.rod" +
" --variant:OldDbsnp " + GATKDataLocation + "Comparisons/Validated/dbSNP/dbsnp_129_b36.rod" +
" -T VariantsToVCF" +
" -L 1:1-30,000,000" +
" -o %s" +

BIN
settings/repository/org.broad/tribble-23.jar → settings/repository/org.broad/tribble-24.jar
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2
settings/repository/org.broad/tribble-23.xml → settings/repository/org.broad/tribble-24.xml
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@ -1,3 +1,3 @@
<ivy-module version="1.0">
<info organisation="org.broad" module="tribble" revision="23" status="integration" />
<info organisation="org.broad" module="tribble" revision="24" status="integration" />
</ivy-module>