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remove the picard DbSNP ROD. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3743 348d0f76-0448-11de-a6fe-93d51630548a
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aaron 2010-07-08 17:46:00 +00:00
parent c80a257f37
commit 12fecc8d8f
2 changed files with 0 additions and 233 deletions
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232
java/src/org/broadinstitute/sting/gatk/refdata/rodPicardDbSNP.java
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@ -1,232 +0,0 @@
/*
* The MIT License
*
* Copyright (c) 2009 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.refdata;
import edu.mit.broad.picard.variation.KnownVariant;
import edu.mit.broad.picard.variation.VariantType;
import edu.mit.broad.picard.variation.DbSnpFileReader;
import org.broadinstitute.sting.utils.GenomeLoc;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.*;
/**
* @author alecw@broadinstitute.org
*/
public class rodPicardDbSNP implements ReferenceOrderedDatum {
private final KnownVariant knownVariant;
private final MyGenomeLoc loc;
private final List<String> alleles;
public rodPicardDbSNP(final KnownVariant knownVariant) {
this.knownVariant = knownVariant;
alleles = Collections.unmodifiableList(Arrays.asList(knownVariant.getObservedAlleles()));
loc = new MyGenomeLoc(knownVariant);
}
/**
* are we bi-allelic?
*/
public boolean isBiallelic() {
return alleles.size() == 2;
}
/**
* get the frequency of this variant, if we're a variant. If we're reference this method
* should return 0. If we can't provide an alternate allele frequency, this should also
* return 0.
* <p/>
* WARNING: This method is only valid for biAllelic data, the contract is to check isBiallelic()
* before calling this method
*
* @return double the minor allele frequency
*/
public double getNonRefAlleleFrequency() {
return knownVariant.getMinorAlleleFrequency();
}
/**
* are we a variant that represents the reference allele?
*
* @return false if we're a variant(indel, delete, SNP, etc), true if we're hom ref
*/
public boolean isReference() {
return false; // snp locations are never "reference", there's always a variant
}
public String getName() {
return "PicarddbSNP";
}
public boolean parseLine(final Object header, final String[] parts) throws IOException {
throw new UnsupportedOperationException("Not a text format so this should never be called.");
}
public String toSimpleString() {
return getName() + ":" + knownVariant.getObservedAllelesString();
}
public String repl() {
throw new UnsupportedOperationException("Not a text format so this should never be called.");
}
/**
* Used by the ROD system to determine how to split input lines
*
* @return Regex string delimiter separating fields
*/
public String delimiterRegex() {
throw new UnsupportedOperationException("Not a text format so this should never be called.");
}
/**
* get the location of this Variant
*
* @return a GenomeLoc
*/
public GenomeLoc getLocation() {
return loc;
}
public int compareTo(final ReferenceOrderedDatum that) {
return getLocation().compareTo(that.getLocation());
}
/**
* Backdoor hook to read header, meta-data, etc. associated with the file. Will be
* called by the ROD system before streaming starts
*
* @param source source data file on disk from which this rod stream will be pulled
* @return a header object that will be passed to parseLine command
*/
public Object initialize(final File source) throws FileNotFoundException {
throw new UnsupportedOperationException("Not a text format so this should never be called.");
}
/**
* get the reference base(s) for this Variant
*
* @return the reference base or bases, as a string
*/
public String getReference() {
// Not known without looking in reference fasta.
return null;
}
/**
* get the -1 * (log 10 of the error value)
*
* @return the postive number space log based error estimate
*/
public double getNegLog10PError() {
// Copied from rodDbSNP
return 4; // -log10(0.0001)
}
/**
* 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
*/
public List<String> getAlternateAlleleList() {
throw new UnsupportedOperationException("Don't know which is the reference allele");
}
/**
* 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. If the reference base is not an allele in this varation
* it will not be in the list (i.e. there is no guarantee that the reference base is in the list).
*
* @return an alternate allele list
*/
public List<String> getAlleleList() {
return alleles;
}
/**
* 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
*/
public char getAlternativeBaseForSNP() {
throw new UnsupportedOperationException("Don't know which is the reference allele");
}
/**
* 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
*/
public char getReferenceForSNP() {
throw new UnsupportedOperationException("Don't know which is the reference allele");
}
public static Iterator<rodPicardDbSNP> createIterator(final String trackName, final File f) throws IOException {
return new rodPicardDbSNPIterator(f);
}
private static class MyGenomeLoc extends GenomeLoc {
private MyGenomeLoc(final KnownVariant knownVariant) {
// GenomeLoc is one-based closed interval.
super(knownVariant.getReferenceSequence(), knownVariant.getSequenceIndex(), knownVariant.getStartPos(),
knownVariant.getEndPos());
}
}
private static class rodPicardDbSNPIterator implements Iterator<rodPicardDbSNP> {
private final DbSnpFileReader reader;
private rodPicardDbSNPIterator(final File f) {
reader = new DbSnpFileReader(f);
}
public boolean hasNext() {
return reader.hasNext();
}
/**
* @return the next element in the iteration.
* @throws NoSuchElementException - iterator has no more elements.
*/
public rodPicardDbSNP next() {
if (!this.hasNext()) throw new NoSuchElementException("rodPicardDbSNP next called on iterator with no more elements");
return new rodPicardDbSNP(reader.next());
}
public void remove() {
reader.remove();
}
}
}

1
java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RODTrackBuilder.java
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@ -57,7 +57,6 @@ public class RODTrackBuilder implements RMDTrackBuilder {
Types.put("Table", TabularROD.class); Types.put("Table", TabularROD.class);
Types.put("HapMap", HapMapROD.class); Types.put("HapMap", HapMapROD.class);
Types.put("Intervals", IntervalRod.class); Types.put("Intervals", IntervalRod.class);
Types.put("PicardDbSNP", rodPicardDbSNP.class);
Types.put("Beagle", BeagleROD.class); Types.put("Beagle", BeagleROD.class);
Types.put("Plink", PlinkRod.class); Types.put("Plink", PlinkRod.class);
} }