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Standardize the dbsnp track name in preparation for case-sensitivity 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3176 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-04-15 19:41:57 +00:00
parent 5f7564bf0a
commit 3330e254a9
14 changed files with 22 additions and 21 deletions
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3
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -47,6 +47,7 @@ import org.broadinstitute.sting.gatk.io.stubs.Stub;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackManager;
import org.broadinstitute.sting.gatk.refdata.utils.RMDIntervalGenerator;
import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.cmdLine.ArgumentException;
@ -331,7 +332,7 @@ public class GenomeAnalysisEngine {
//
// please don't use these in the future, use the new syntax <- if we're not using these please remove them
//
if (argCollection.DBSNPFile != null) bindConvenienceRods("dbSNP", "dbsnp", argCollection.DBSNPFile);
if (argCollection.DBSNPFile != null) bindConvenienceRods(rodDbSNP.STANDARD_DBSNP_TRACK_NAME, "dbsnp", argCollection.DBSNPFile);
if (argCollection.HAPMAPFile != null)
bindConvenienceRods("hapmap", "HapMapAlleleFrequencies", argCollection.HAPMAPFile);
if (argCollection.HAPMAPChipFile != null)

3
java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
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@ -19,6 +19,9 @@ import java.util.List;
* To change this template use File | Settings | File Templates.
*/
public class rodDbSNP extends BasicReferenceOrderedDatum implements VariationRod {
public static final String STANDARD_DBSNP_TRACK_NAME = "dbsnp";
public GenomeLoc loc; // genome location of SNP
// Reference sequence chromosome or scaffold
// Start and stop positions in chrom

2
java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
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@ -148,7 +148,7 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
}
String rodString = Utils.join(", ", rodStrings);
rodDbSNP dbsnp = tracker.lookup("dbSNP",rodDbSNP.class);
rodDbSNP dbsnp = tracker.lookup(rodDbSNP.STANDARD_DBSNP_TRACK_NAME,rodDbSNP.class);
if ( dbsnp != null)
rodString += dbsnp.toMediumString();

2
java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java
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@ -33,7 +33,7 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
if ( tracker == null || !BaseUtils.isRegularBase(ref.getBase()) )
return 0;
rodDbSNP dbsnp = rodDbSNP.getFirstRealSNP(tracker.getReferenceMetaData("dbsnp"));
rodDbSNP dbsnp = rodDbSNP.getFirstRealSNP(tracker.getReferenceMetaData(rodDbSNP.STANDARD_DBSNP_TRACK_NAME));
Allele refAllele = new Allele(Character.toString(ref.getBase()), true);
Collection<VariantContext> contexts = tracker.getVariantContexts(INPUT_ROD_NAME, ALLOWED_VARIANT_CONTEXT_TYPES, context.getLocation(), refAllele, true, false);

2
java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
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@ -156,7 +156,7 @@ public class VariantAnnotatorEngine {
// annotate dbsnp occurrence
if ( annotateDbsnp ) {
rodDbSNP dbsnp = rodDbSNP.getFirstRealSNP(tracker.getReferenceMetaData("dbsnp"));
rodDbSNP dbsnp = rodDbSNP.getFirstRealSNP(tracker.getReferenceMetaData(rodDbSNP.STANDARD_DBSNP_TRACK_NAME));
infoAnnotations.put(VCFRecord.DBSNP_KEY, dbsnp == null ? "0" : "1");
// annotate dbsnp id if available and not already there
if ( dbsnp != null && !vc.hasAttribute("ID") )

2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModel.java
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@ -112,6 +112,6 @@ public abstract class GenotypeCalculationModel implements Cloneable {
* @return the dbsnp rod if there is one at this position
*/
public static rodDbSNP getDbSNP(RefMetaDataTracker tracker) {
return rodDbSNP.getFirstRealSNP(tracker.getReferenceMetaData("dbsnp"));
return rodDbSNP.getFirstRealSNP(tracker.getReferenceMetaData(rodDbSNP.STANDARD_DBSNP_TRACK_NAME));
}
}

3
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
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@ -19,6 +19,7 @@ import net.sf.samtools.util.SequenceUtil;
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.Requires;
@ -152,7 +153,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
// Warn the user if a dbSNP file was specified since it isn't being used here
boolean foundDBSNP = false;
for( ReferenceOrderedDataSource rod : this.getToolkit().getRodDataSources() ) {
if( rod.getName().equalsIgnoreCase( "dbsnp" ) ) {
if( rod.getName().equalsIgnoreCase(rodDbSNP.STANDARD_DBSNP_TRACK_NAME) ) {
foundDBSNP = true;
}
}

2
java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java
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@ -43,7 +43,7 @@ public class PickSequenomProbes extends RefWalker<String, String> {
if ( SNP_MASK != null ) {
logger.info("Loading SNP mask... ");
ReferenceOrderedData snp_mask;
if ( SNP_MASK.contains("dbsnp")) {
if ( SNP_MASK.contains(rodDbSNP.STANDARD_DBSNP_TRACK_NAME)) {
snp_mask = new ReferenceOrderedData<rodDbSNP>("snp_mask",new java.io.File(SNP_MASK),rodDbSNP.class);
} else {
snp_mask = new ReferenceOrderedData<TabularROD>("snp_mask",

2
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ValidationDataAnalysis.java
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@ -15,7 +15,7 @@ import java.util.List;
* To change this template use File | Settings | File Templates.
*/
// @Allows(value={DataSource.REFERENCE},referenceMetaData = {@RMD(name="eval",type=VariationRod.class), @RMD(name="dbsnp",type= rodDbSNP.class),@RMD(name="hapmap-chip",type=RodGenotypeChipAsGFF.class), @RMD(name="interval",type=IntervalRod.class), @RMD(name="validation",type=RodGenotypeChipAsGFF.class)})
// @Allows(value={DataSource.REFERENCE},referenceMetaData = {@RMD(name="eval",type=VariationRod.class), @RMD(name=rodDbSNP.STANDARD_DBSNP_TRACK_NAME,type= rodDbSNP.class),@RMD(name="hapmap-chip",type=RodGenotypeChipAsGFF.class), @RMD(name="interval",type=IntervalRod.class), @RMD(name="validation",type=RodGenotypeChipAsGFF.class)})
public class ValidationDataAnalysis extends BasicVariantAnalysis implements GenotypeAnalysis, PopulationAnalysis {
private int calls_at_validated_sites = 0;

3
java/src/org/broadinstitute/sting/oneoffprojects/multisamplecaller/MultiSampleCaller.java
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@ -8,6 +8,7 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
@ -881,7 +882,7 @@ public class MultiSampleCaller extends LocusWalker<MultiSampleCaller.MultiSample
MultiSampleCallResult MultiSampleCall(RefMetaDataTracker tracker, char ref, AlignmentContext context, List<String> sample_names)
{
String in_dbsnp;
if (tracker.getReferenceMetaData("DBSNP").size() > 0) { in_dbsnp = "known"; } else { in_dbsnp = "novel"; }
if (tracker.getReferenceMetaData(rodDbSNP.STANDARD_DBSNP_TRACK_NAME).size() > 0) { in_dbsnp = "known"; } else { in_dbsnp = "novel"; }
AlignmentContext[] contexts = filterAlignmentContext(context, sample_names, 0);
glCache.clear(); // reset the cache

4
java/src/org/broadinstitute/sting/oneoffprojects/walkers/ValidateDbSNPConversion.java
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@ -20,8 +20,8 @@ import java.io.PrintStream;
public class ValidateDbSNPConversion extends RefWalker<Pair<Matrix.BASE, Matrix.BASE>, Matrix> {
@Override
public Pair<Matrix.BASE, Matrix.BASE> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if (!tracker.hasROD("dbsnp")) return null;
rodDbSNP rod = tracker.lookup("dbSNP",rodDbSNP.class);
if (!tracker.hasROD(rodDbSNP.STANDARD_DBSNP_TRACK_NAME)) return null;
rodDbSNP rod = tracker.lookup(rodDbSNP.STANDARD_DBSNP_TRACK_NAME,rodDbSNP.class);
if (rod != null && rod.isSNP() && rod.isBiallelic()) {
return new Pair<Matrix.BASE, Matrix.BASE>(Matrix.BASE.toBase((byte) ref.getBase()), Matrix.BASE.toBase((byte) rod.getAlternativeBaseForSNP()));
}

7
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/TiTvVariantEvaluator.java
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@ -7,9 +7,6 @@ import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
import java.util.List;
import java.util.Arrays;
@Analysis(name = "Ti/Tv Variant Evaluator", description = "Ti/Tv Variant Evaluator")
public class TiTvVariantEvaluator extends VariantEvaluator {
@ -58,10 +55,6 @@ public class TiTvVariantEvaluator extends VariantEvaluator {
if (vc1 != null) updateTiTv(vc1, false);
if (vc2 != null) updateTiTv(vc2, true);
//if ( vc1 == null && vc2 != null && vc2.isSNP() && vc2.isBiallelic() )
// System.out.printf("VC2 = %s%n", vc2);
//if ( vc2 != null && vc2.getName().equals("dbsnp") )
return null; // we don't capture any intersting sites
}

5
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java
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@ -9,6 +9,7 @@ import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.playground.utils.report.ReportMarshaller;
import org.broadinstitute.sting.playground.utils.report.VE2ReportFactory;
@ -95,7 +96,7 @@ public class VariantEval2Walker extends RodWalker<Integer, Integer> {
protected String[] SELECT_NAMES = {};
@Argument(shortName="known", doc="Name of ROD bindings containing variant sites that should be treated as known when splitting eval rods into known and novel subsets", required=false)
protected String[] KNOWN_NAMES = {"dbsnp"};
protected String[] KNOWN_NAMES = {rodDbSNP.STANDARD_DBSNP_TRACK_NAME};
@Argument(shortName="sample", doc="Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context", required=false)
protected String[] SAMPLES = {};
@ -238,7 +239,7 @@ public class VariantEval2Walker extends RodWalker<Integer, Integer> {
for ( ReferenceOrderedDataSource d : this.getToolkit().getRodDataSources() ) {
if ( d.getName().startsWith("eval") ) {
evalNames.add(d.getName());
} else if ( d.getName().startsWith("dbsnp") || d.getName().startsWith("hapmap") || d.getName().startsWith("comp") ) {
} else if ( d.getName().startsWith(rodDbSNP.STANDARD_DBSNP_TRACK_NAME) || d.getName().startsWith("hapmap") || d.getName().startsWith("comp") ) {
compNames.add(d.getName());
} else {
logger.info("Not evaluating ROD binding " + d.getName());

3
java/src/org/broadinstitute/sting/playground/gatk/walkers/DeNovoSNPWalker.java
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@ -7,6 +7,7 @@ import org.broadinstitute.sting.gatk.contexts.variantcontext.Genotype;
import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.VariationRod;
import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper;
import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext;
@ -45,7 +46,7 @@ public class DeNovoSNPWalker extends RefWalker<String, Integer>{
public String map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
VariationRod child = tracker.lookup("child",VariationRod.class);
VariationRod dbsnp = tracker.lookup("dbSNP",VariationRod.class);
VariationRod dbsnp = tracker.lookup(rodDbSNP.STANDARD_DBSNP_TRACK_NAME,VariationRod.class);
if (child != null) {
if (child.isSNP() && child.getNegLog10PError() > 5) { // BTR > 5