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half-way through making rodDbSNP implement AllelicVariant interface; does not work yet 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@267 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-04-02 20:48:59 +00:00
parent 4faa680887
commit 4bc035d919
1 changed files with 70 additions and 4 deletions
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74
java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
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@ -7,6 +7,7 @@ import java.util.*;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.gatk.refdata.AllelicVariant;
/**
* Example format:
@ -18,7 +19,7 @@ import org.broadinstitute.sting.utils.Utils;
* Time: 10:47:14 AM
* To change this template use File | Settings | File Templates.
*/
public class rodDbSNP extends ReferenceOrderedDatum {
public class rodDbSNP extends ReferenceOrderedDatum implements AllelicVariant {
public GenomeLoc loc; // genome location of SNP
// Reference sequence chromosome or scaffold
// Start and stop positions in chrom
@ -64,14 +65,31 @@ public class rodDbSNP extends ReferenceOrderedDatum {
return strand.equals("+");
}
// Get the reference bases on the forward strand
public String getRefBasesFWD() {
/** Returns bases in the reference allele as a String. String can be empty (as in insertion into
* the reference), can contain a single character (as in SNP or one-base deletion), or multiple characters
* (for longer indels).
*
* @return reference allele, forward strand
*/
public String getRefBasesFWD() {
if ( onFwdStrand() )
return refBases;
else
return SequenceUtil.reverseComplement(refBases);
}
/**
* Returns reference (major) allele base for a SNP variant as a character; should throw IllegalStateException
* if variant is not a SNP.
*
* @return reference base on the forward strand
*/
public char getRefSnpFWD() throws IllegalStateException {
if ( isIndel() ) throw new IllegalStateException("Variant is not a SNP");
if ( onFwdStrand() ) return refBases.charAt(0);
else return SequenceUtil.reverseComplement(refBases).charAt(0);
}
public List<String> getAllelesFWD() {
List<String> alleles = null;
if ( onFwdStrand() )
@ -95,7 +113,7 @@ public class rodDbSNP extends ReferenceOrderedDatum {
public boolean isSNP() { return varType.contains("single"); }
public boolean isInsertion() { return varType.contains("insertion"); }
public boolean isDeletion() { return varType.contains("deletion"); }
public boolean isIndel() { return varType.contains("in-del"); }
public boolean isIndel() { return isInsertion() || isDeletion() || varType.contains("in-del"); }
public boolean isHapmap() { return validationStatus.contains("by-hapmap"); }
public boolean is2Hit2Allele() { return validationStatus.contains("by-2hit-2allele"); }
@ -154,4 +172,52 @@ public class rodDbSNP extends ReferenceOrderedDatum {
throw e;
}
}
@Override
public String getAltBasesFWD() {
// TODO Auto-generated method stub
return null;
}
@Override
public char getAltSnpFWD() throws IllegalStateException {
// TODO Auto-generated method stub
return 0;
}
@Override
public double getConsensusConfidence() {
// TODO Auto-generated method stub
return 0;
}
@Override
public List<String> getGenotype() throws IllegalStateException {
// TODO Auto-generated method stub
return null;
}
@Override
public double getMAF() {
// TODO Auto-generated method stub
return 0;
}
@Override
public int getPloidy() throws IllegalStateException {
// TODO Auto-generated method stub
return 0;
}
@Override
public double getVariationConfidence() {
// TODO Auto-generated method stub
return 0;
}
@Override
public boolean isGenotype() {
// TODO Auto-generated method stub
return false;
}
}