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Added convenience methods in RodVCF to pull out all of the VCF data from the VCFRecord (e.g. getID(), getSamples(), getInfoValues()) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2374 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-12-16 17:58:41 +00:00
parent bb312814a2
commit e051311e8c
1 changed files with 51 additions and 0 deletions
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51
java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
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@ -13,6 +13,7 @@ import java.io.IOException;
import java.util.Iterator; import java.util.Iterator;
import java.util.List; import java.util.List;
import java.util.NoSuchElementException; import java.util.NoSuchElementException;
import java.util.Map;
/** /**
@ -104,6 +105,11 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
return mCurrentRecord.getType(); return mCurrentRecord.getType();
} }
public String getID() {
assertNotNull();
return mCurrentRecord.getID();
}
/** /**
* are we a SNP? If not we're a Indel/deletion * are we a SNP? If not we're a Indel/deletion
* *
@ -166,6 +172,16 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
return mCurrentRecord.getNegLog10PError(); return mCurrentRecord.getNegLog10PError();
} }
public double getQual() {
assertNotNull();
return mCurrentRecord.getQual();
}
public boolean hasAlternateAllele() {
assertNotNull();
return mCurrentRecord.hasAlternateAllele();
}
/** /**
* gets the alternate alleles. This method should return all the alleles present at the location, * 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 * NOT including the reference base. This is returned as a string list with no guarantee ordering
@ -232,6 +248,11 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
return mCurrentRecord.getReferenceForSNP(); return mCurrentRecord.getReferenceForSNP();
} }
public boolean hasGenotypeData() {
assertNotNull();
return mCurrentRecord.hasGenotypeData();
}
/** /**
* get the genotype * get the genotype
* *
@ -275,6 +296,36 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
return mCurrentRecord.hasGenotype(x); return mCurrentRecord.hasGenotype(x);
} }
public String[] getSampleNames() {
assertNotNull();
return mCurrentRecord.getSampleNames();
}
public Map<String, String> getInfoValues() {
assertNotNull();
return mCurrentRecord.getInfoValues();
}
public String[] getFilteringCodes() {
assertNotNull();
return mCurrentRecord.getFilteringCodes();
}
public boolean isFiltered() {
assertNotNull();
return mCurrentRecord.isFiltered();
}
public boolean hasFilteringCodes() {
assertNotNull();
return mCurrentRecord.hasFilteringCodes();
}
public String getFilterString() {
assertNotNull();
return mCurrentRecord.getFilterString();
}
public VCFHeader getHeader() { public VCFHeader getHeader() {
return mReader.getHeader(); return mReader.getHeader();
} }