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Removed outdated Sequenom rod and renamed HapMapGenotypeROD to HapMapROD. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3149 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-04-11 01:43:07 +00:00
parent fa01876255
commit 961ca05abc
6 changed files with 8 additions and 148 deletions
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4
java/src/org/broadinstitute/sting/gatk/refdata/HapMapGenotypeROD.java → java/src/org/broadinstitute/sting/gatk/refdata/HapMapROD.java
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@ -5,9 +5,9 @@ import java.util.*;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
public class HapMapGenotypeROD extends TabularROD
public class HapMapROD extends TabularROD
{
public HapMapGenotypeROD(final String name) {
public HapMapROD(final String name) {
super(name);
}

139
java/src/org/broadinstitute/sting/gatk/refdata/SequenomROD.java
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@ -1,139 +0,0 @@
package org.broadinstitute.sting.gatk.refdata;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.genotype.Variation;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
public class SequenomROD extends TabularROD implements Variation {
public SequenomROD(String name) {
super(name);
}
public GenomeLoc getLocation() {
long pos = Long.parseLong(this.get("1"));
return GenomeLocParser.createGenomeLoc(this.get("0"), pos);
}
/**
* get the reference base(s) at this position
*
* @return the reference base or bases, as a string
*/
@Override
public String getReference() {
return "";
}
public List<String> getFWDAlleles() {
return Arrays.asList(this.get("2"));
}
public String getAltBasesFWD() { return getFWDAlleles().get(0); }
/**
* get the frequency of this variant, if we're a variant. If we're reference this method
* should return 0.
*
* @return double with the stored frequency
*/
@Override
public double getNonRefAlleleFrequency() {
return 0.0;
}
/**
* A convenience method, for switching over the variation type
*
* @return the VARIANT_TYPE of the current variant
*/
@Override
public VARIANT_TYPE getType() {
return VARIANT_TYPE.SNP;
}
public boolean isSNP() { return true; }
public boolean isReference() { return false; }
public boolean isInsertion() { return false; }
public boolean isDeletion() { return false; }
public boolean isIndel() { return false; }
/**
* gets the alternate base is the case of a SNP. Throws an IllegalStateException if we're not a SNP
* of
*
* @return a char, representing the alternate base
*/
@Override
public char getAlternativeBaseForSNP() {
return getAltBasesFWD().charAt(0);
}
/**
* gets the reference base is the case of a SNP. Throws an IllegalStateException if we're not a SNP
*
* @return a char, representing the alternate base
*/
@Override
public char getReferenceForSNP() {
return 'N';
}
public boolean isBiallelic() { return true; }
/**
* get the -1 * (log 10 of the error value)
*
* @return the postive number space log based error estimate
*/
@Override
public double getNegLog10PError() {
return 0.0;
}
/**
* gets the alternate alleles. This method should return all the alleles present at the location,
* NOT including the reference base. This is returned as a string list with no guarantee ordering
* of alleles (i.e. the first alternate allele is not always going to be the allele with the greatest
* frequency).
*
* @return an alternate allele list
*/
@Override
public List<String> getAlternateAlleleList() {
List<String> ret = new ArrayList<String>();
for (char c: getAltBasesFWD().toCharArray())
ret.add(String.valueOf(c));
return ret;
}
/**
* gets the alleles. This method should return all the alleles present at the location,
* including the reference base. The first allele should always be the reference allele, followed
* by an unordered list of alternate alleles.
*
* @return an alternate allele list
*/
@Override
public List<String> getAlleleList() {
throw new StingException("SequenomRod doesn't know of the reference, and can't generate allele lists");
}
public boolean isHom() { return false; }
public boolean isHet() { return false; }
public double getHeterozygosity() { return 0.0; }
public double getMAF() { return 0.0; }
public int getPloidy() { return 2; }
public int length() { return 1; }
public String toString() {
StringBuffer sb = new StringBuffer();
sb.append(getLocation().getContig() + "\t" + getLocation().getStart() + "\t" + getFWDAlleles().get(0));
return sb.toString();
}
}

4
java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
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@ -43,7 +43,7 @@ public class VariantContextAdaptors {
adaptors.put(RodVCF.class, new RodVCFAdaptor());
adaptors.put(VCFRecord.class, new VCFRecordAdaptor());
adaptors.put(PlinkRod.class, new PlinkRodAdaptor());
adaptors.put(HapMapGenotypeROD.class, new HapMapAdaptor());
adaptors.put(HapMapROD.class, new HapMapAdaptor());
adaptors.put(RodGLF.class, new GLFAdaptor());
adaptors.put(RodGeliText.class, new GeliAdaptor());
}
@ -604,7 +604,7 @@ public class VariantContextAdaptors {
* @return a VariantContext object
*/
VariantContext convert(String name, Object input, Allele refAllele) {
HapMapGenotypeROD hapmap = (HapMapGenotypeROD)input;
HapMapROD hapmap = (HapMapROD)input;
// add the reference allele
HashSet<Allele> alleles = new HashSet<Allele>();

3
java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RODTrackBuilder.java
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@ -63,11 +63,10 @@ public class RODTrackBuilder implements RMDTrackBuilder {
Types.put("Table", TabularROD.class);
Types.put("PooledEM", PooledEMSNPROD.class);
Types.put("CleanedOutSNP", CleanedOutSNPROD.class);
Types.put("Sequenom", SequenomROD.class);
Types.put("SangerSNP", SangerSNPROD.class);
Types.put("SimpleIndel", SimpleIndelROD.class);
Types.put("PointIndel", PointIndelROD.class);
Types.put("HapMapGenotype", HapMapGenotypeROD.class);
Types.put("HapMap", HapMapROD.class);
Types.put("Intervals", IntervalRod.class);
Types.put("Variants", RodGeliText.class);
Types.put("GLF", RodGLF.class);

4
java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java
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@ -70,8 +70,8 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
Object rod = rods.get(0);
if ( rod instanceof RodVCF )
samples.addAll(Arrays.asList(((RodVCF)rod).getSampleNames()));
else if ( rod instanceof HapMapGenotypeROD )
samples.addAll(Arrays.asList(((HapMapGenotypeROD)rod).getSampleIDs()));
else if ( rod instanceof HapMapROD )
samples.addAll(Arrays.asList(((HapMapROD)rod).getSampleIDs()));
else
samples.addAll(Arrays.asList(rec.getSampleNames()));
}

2
java/test/org/broadinstitute/sting/gatk/walkers/VariantsToVCFIntegrationTest.java
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@ -58,7 +58,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + oneKGLocation + "reference/human_b36_both.fasta" +
" -B variant,HapMapGenotype," + validationDataLocation + "rawHapMap.yri.chr1.txt" +
" -B variant,HapMap," + validationDataLocation + "rawHapMap.yri.chr1.txt" +
" -T VariantsToVCF" +
" -L 1:1-1,000,000" +
" -o %s",