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This rod was all wrong for generating the alternate snp alleles (it returned null or even the wrong value); fixed. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1531 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-09-04 14:21:46 +00:00
parent a08c68362e
commit 849dce799d
1 changed files with 9 additions and 17 deletions
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26
java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
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@ -4,11 +4,7 @@ import net.sf.picard.util.SequenceUtil;
import java.util.*;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.MalformedGenomeLocException;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.gatk.refdata.AllelicVariant;
import org.broadinstitute.sting.utils.*;
/**
* Example format:
@ -165,8 +161,10 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
loc = GenomeLocParser.parseGenomeLoc(contig, start, stop-1);
name = parts[4];
refBases = parts[5];
strand = parts[6];
refBases = parts[7];
if ( strand == "-" )
refBases = BaseUtils.simpleReverseComplement(refBases);
observed = parts[9];
molType = parts[10];
varType = parts[11];
@ -190,24 +188,22 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
}
}
@Override
public String getAltBasesFWD() {
// TODO Auto-generated method stub
return null;
List<String> alleles = getAllelesFWD();
return (alleles.get(0).equals(refBases) ? alleles.get(1) : alleles.get(0));
}
@Override
public char getAltSnpFWD() throws IllegalStateException {
return getAllelesFWD().get(1).charAt(0);
if ( !isSNP() )
throw new IllegalStateException("I'm not a SNP");
return getAltBasesFWD().charAt(0);
}
@Override
public double getConsensusConfidence() {
// TODO Auto-generated method stub
return Double.MAX_VALUE;
}
@Override
public List<String> getGenotype() throws IllegalStateException {
return Arrays.asList(Utils.join("", getAllelesFWD()));
}
@ -222,25 +218,21 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
return avHet;
}
@Override
public int getPloidy() throws IllegalStateException {
// TODO Auto-generated method stub
return 0;
}
@Override
public double getVariationConfidence() {
// TODO Auto-generated method stub
return Double.MAX_VALUE;
}
@Override
public boolean isGenotype() {
// TODO Auto-generated method stub
return false;
}
@Override
public boolean isBiallelic() {
// TODO Auto-generated method stub
return observed.indexOf('/')==observed.lastIndexOf('/');