zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

26
java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
View File

@ -4,11 +4,7 @@ import net.sf.picard.util.SequenceUtil;
import java.util.*; import java.util.*;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.*;
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;
/** /**
* Example format: * Example format:
@ -165,8 +161,10 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
loc = GenomeLocParser.parseGenomeLoc(contig, start, stop-1); loc = GenomeLocParser.parseGenomeLoc(contig, start, stop-1);
name = parts[4]; name = parts[4];
refBases = parts[5];
strand = parts[6]; strand = parts[6];
refBases = parts[7];
if ( strand == "-" )
refBases = BaseUtils.simpleReverseComplement(refBases);
observed = parts[9]; observed = parts[9];
molType = parts[10]; molType = parts[10];
varType = parts[11]; varType = parts[11];
@ -190,24 +188,22 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
} }
} }
@Override
public String getAltBasesFWD() { public String getAltBasesFWD() {
// TODO Auto-generated method stub List<String> alleles = getAllelesFWD();
return null; return (alleles.get(0).equals(refBases) ? alleles.get(1) : alleles.get(0));
} }
@Override
public char getAltSnpFWD() throws IllegalStateException { 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() { public double getConsensusConfidence() {
// TODO Auto-generated method stub // TODO Auto-generated method stub
return Double.MAX_VALUE; return Double.MAX_VALUE;
} }
@Override
public List<String> getGenotype() throws IllegalStateException { public List<String> getGenotype() throws IllegalStateException {
return Arrays.asList(Utils.join("", getAllelesFWD())); return Arrays.asList(Utils.join("", getAllelesFWD()));
} }
@ -222,25 +218,21 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
return avHet; return avHet;
} }
@Override
public int getPloidy() throws IllegalStateException { public int getPloidy() throws IllegalStateException {
// TODO Auto-generated method stub // TODO Auto-generated method stub
return 0; return 0;
} }
@Override
public double getVariationConfidence() { public double getVariationConfidence() {
// TODO Auto-generated method stub // TODO Auto-generated method stub
return Double.MAX_VALUE; return Double.MAX_VALUE;
} }
@Override
public boolean isGenotype() { public boolean isGenotype() {
// TODO Auto-generated method stub // TODO Auto-generated method stub
return false; return false;
} }
@Override
public boolean isBiallelic() { public boolean isBiallelic() {
// TODO Auto-generated method stub // TODO Auto-generated method stub
return observed.indexOf('/')==observed.lastIndexOf('/'); return observed.indexOf('/')==observed.lastIndexOf('/');