Almost done removing any trace of the old Variation and Genotype interfaces.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3202 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron
parent
7902db616e
commit
b5f6f54968
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@ -46,7 +46,7 @@ import java.util.NoSuchElementException;
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* <p/>
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* the rod class for GLF data.
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*/
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public class RodGLF implements VariationRod, Iterator<RodGLF> {
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public class RodGLF implements Iterator<RodGLF>, ReferenceOrderedDatum {
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public GLFReader mReader;
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private final String mName;
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private GenomeLoc mLoc;
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@ -61,7 +61,6 @@ public class RodGLF implements VariationRod, Iterator<RodGLF> {
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*
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* @return the name
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*/
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@Override
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public String getName() {
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return mName;
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}
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@ -74,13 +73,11 @@ public class RodGLF implements VariationRod, Iterator<RodGLF> {
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*
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* @return a header object that will be passed to parseLine command
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*/
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@Override
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public Object initialize(File source) throws FileNotFoundException {
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mReader = new GLFReader(source);
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return null;
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}
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@Override
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public String toSimpleString() {
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return toString();
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}
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@ -109,7 +106,6 @@ public class RodGLF implements VariationRod, Iterator<RodGLF> {
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);
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}
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@Override
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public String repl() {
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return this.toString();
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}
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@ -119,7 +115,6 @@ public class RodGLF implements VariationRod, Iterator<RodGLF> {
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*
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* @return Regex string delimiter separating fields
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*/
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@Override
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public String delimiterRegex() {
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return "";
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}
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@ -129,7 +124,6 @@ public class RodGLF implements VariationRod, Iterator<RodGLF> {
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*
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* @return the geonome loc
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*/
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@Override
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public GenomeLoc getLocation() {
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return mLoc;
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}
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@ -139,13 +133,11 @@ public class RodGLF implements VariationRod, Iterator<RodGLF> {
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*
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* @return the reference base or bases, as a string
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*/
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@Override
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public String getReference() {
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return mRecord.getRefBase().toString();
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}
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/** are we bi-allelic? */
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@Override
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public boolean isBiallelic() {
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return true;
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}
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@ -157,7 +149,6 @@ public class RodGLF implements VariationRod, Iterator<RodGLF> {
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*
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* @return
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*/
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@Override
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public boolean isReference() {
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return (!isSNP());
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}
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@ -167,7 +158,6 @@ public class RodGLF implements VariationRod, Iterator<RodGLF> {
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*
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* @return true if we're an insertion or deletion
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*/
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@Override
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public boolean isIndel() {
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return (isDeletion() || isInsertion());
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}
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@ -178,7 +168,6 @@ public class RodGLF implements VariationRod, Iterator<RodGLF> {
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*
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* @return a char, representing the alternate base
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*/
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@Override
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public char getAlternativeBaseForSNP() {
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if (!this.isSNP()) throw new IllegalStateException("we're not a SNP");
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List<String> alleles = this.getAlternateAlleleList();
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@ -191,7 +180,6 @@ public class RodGLF implements VariationRod, Iterator<RodGLF> {
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*
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* @return a char, representing the alternate base
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*/
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@Override
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public char getReferenceForSNP() {
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if (!this.isSNP()) throw new IllegalStateException("we're not a SNP");
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return Utils.stringToChar(getReference());
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@ -202,7 +190,6 @@ public class RodGLF implements VariationRod, Iterator<RodGLF> {
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*
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* @return true or false
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*/
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@Override
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public boolean isSNP() {
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return ((mRecord.getRecordType() == GLFRecord.RECORD_TYPE.SINGLE) &&
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(!getBestGenotype(1).toString().equals(refString(mRecord.getRefBase().toChar()))));
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@ -251,7 +238,6 @@ public class RodGLF implements VariationRod, Iterator<RodGLF> {
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*
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* @return true or false
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*/
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@Override
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public boolean isInsertion() {
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return ((mRecord.getRecordType() == GLFRecord.RECORD_TYPE.VARIABLE) &&
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((GLFVariableLengthCall) mRecord).getIndelLen1() > 0);
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@ -263,7 +249,6 @@ public class RodGLF implements VariationRod, Iterator<RodGLF> {
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*
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* @return true or false
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*/
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@Override
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public boolean isDeletion() {
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return ((mRecord.getRecordType() == GLFRecord.RECORD_TYPE.VARIABLE) &&
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((GLFVariableLengthCall) mRecord).getIndelLen1() < 0);
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@ -274,27 +259,15 @@ public class RodGLF implements VariationRod, Iterator<RodGLF> {
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*
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* @return
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*/
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@Override
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public double getNonRefAlleleFrequency() {
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return 0;
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}
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/** @return the VARIANT_TYPE of the current variant */
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@Override
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public VARIANT_TYPE getType() {
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if (this.isSNP()) return VARIANT_TYPE.SNP;
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else if (this.isInsertion()) return VARIANT_TYPE.INSERTION;
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else if (this.isDeletion()) return VARIANT_TYPE.DELETION;
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else return VARIANT_TYPE.REFERENCE;
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}
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/**
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* Returns phred-mapped confidence in variation event (e.g. MAQ's SNP confidence, or AlleleCaller's best vs. ref).
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*
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* @return
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*/
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@Override
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public double getNegLog10PError() {
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String ref = new String() + mRecord.getRefBase() + mRecord.getRefBase();
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int index = 0;
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@ -313,7 +286,6 @@ public class RodGLF implements VariationRod, Iterator<RodGLF> {
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*
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* @return an alternate allele list
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*/
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@Override
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public List<String> getAlternateAlleleList() {
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LikelihoodObject.GENOTYPE genotype = getBestGenotype(1);
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List<String> ret = new ArrayList<String>();
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@ -330,7 +302,6 @@ public class RodGLF implements VariationRod, Iterator<RodGLF> {
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*
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* @return an alternate allele list
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*/
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@Override
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public List<String> getAlleleList() {
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LikelihoodObject.GENOTYPE genotype = getBestGenotype(1);
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List<String> list = new ArrayList<String>();
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@ -345,7 +316,6 @@ public class RodGLF implements VariationRod, Iterator<RodGLF> {
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return 1;
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}
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@Override
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public int compareTo(ReferenceOrderedDatum that) {
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return this.mLoc.compareTo(that.getLocation());
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}
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@ -359,7 +329,6 @@ public class RodGLF implements VariationRod, Iterator<RodGLF> {
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* @return false, alwayss
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* @throws java.io.IOException
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*/
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@Override
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public boolean parseLine(Object header, String[] parts) throws IOException {
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return false; //To change body of implemented methods use File | Settings | File Templates.
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}
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@ -36,7 +36,7 @@ import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.List;
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public class RodGeliText extends BasicReferenceOrderedDatum implements Variation {
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public class RodGeliText extends BasicReferenceOrderedDatum {
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public enum Genotype_Strings {
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AA, AC, AG, AT, CC, CG, CT, GG, GT, TT
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}
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@ -195,11 +195,6 @@ public class RodGeliText extends BasicReferenceOrderedDatum implements Variation
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return 1.0;
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}
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/** @return the VARIANT_TYPE of the current variant */
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public Variation.VARIANT_TYPE getType() {
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return Variation.VARIANT_TYPE.SNP;
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}
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public boolean isSNP() {
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if (this.getReference().length() == 1)
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return (this.refBase != this.bestGenotype.charAt(0) || this.refBase != this.bestGenotype.charAt(1));
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@ -4,9 +4,8 @@ import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import org.broadinstitute.sting.utils.StingException;
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import org.broadinstitute.sting.utils.Utils;
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import org.broadinstitute.sting.utils.genotype.BasicGenotype;
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import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
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import org.broadinstitute.sting.utils.genotype.Genotype;
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import org.broadinstitute.sting.utils.genotype.Variation;
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import java.util.*;
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import java.util.regex.MatchResult;
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@ -20,7 +19,7 @@ import java.util.regex.Pattern;
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* Time: 10:47:14 AM
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* To change this template use File | Settings | File Templates.
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*/
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public class RodGenotypeChipAsGFF extends BasicReferenceOrderedDatum implements VariationRod {
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public class RodGenotypeChipAsGFF extends BasicReferenceOrderedDatum {
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private String contig, source, feature, strand, frame;
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private long start, stop;
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private double score;
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@ -83,7 +82,7 @@ public class RodGenotypeChipAsGFF extends BasicReferenceOrderedDatum implements
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*
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* @return the reference base or bases, as a string
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*/
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@Override
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public String getReference() {
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throw new IllegalStateException("Chip data is unable to determine the reference");
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}
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@ -93,7 +92,7 @@ public class RodGenotypeChipAsGFF extends BasicReferenceOrderedDatum implements
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*
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* @return the log based error estimate
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*/
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@Override
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public double getNegLog10PError() {
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return 4; // 1/10000 error
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}
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@ -106,7 +105,7 @@ public class RodGenotypeChipAsGFF extends BasicReferenceOrderedDatum implements
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*
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* @return an alternate allele list
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*/
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@Override
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public List<String> getAlternateAlleleList() {
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throw new StingException("Hapmap is unable to provide an alternate allele list; the reference is unknown");
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}
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@ -118,7 +117,7 @@ public class RodGenotypeChipAsGFF extends BasicReferenceOrderedDatum implements
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*
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* @return an alternate allele list
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*/
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@Override
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public List<String> getAlleleList() {
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List<String> ret = new ArrayList<String>();
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for (char c : feature.toCharArray())
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@ -216,17 +215,11 @@ public class RodGenotypeChipAsGFF extends BasicReferenceOrderedDatum implements
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*
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* @return VariantFrequency with the stored frequency
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*/
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@Override
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public double getNonRefAlleleFrequency() {
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return this.getMAF();
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}
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/** @return the VARIANT_TYPE of the current variant */
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@Override
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public VARIANT_TYPE getType() {
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return VARIANT_TYPE.SNP;
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}
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public boolean isSNP() { return false; }
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public boolean isInsertion() { return false; }
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public boolean isDeletion() { return false; }
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@ -238,7 +231,7 @@ public class RodGenotypeChipAsGFF extends BasicReferenceOrderedDatum implements
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*
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* @return a char, representing the alternate base
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*/
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@Override
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public char getAlternativeBaseForSNP() {
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return this.getAltSnpFWD();
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}
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@ -248,7 +241,7 @@ public class RodGenotypeChipAsGFF extends BasicReferenceOrderedDatum implements
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*
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* @return a char, representing the alternate base
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*/
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@Override
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public char getReferenceForSNP() {
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return this.getRefSnpFWD();
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}
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@ -267,25 +260,6 @@ public class RodGenotypeChipAsGFF extends BasicReferenceOrderedDatum implements
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public boolean isBiallelic() { return true; }
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public int length() { return 1; }
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/**
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* get the genotype
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*
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* @return a map in lexigraphical order of the genotypes
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*/
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public Genotype getCalledGenotype() {
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return new BasicGenotype(this.getLocation(),this.feature,Character.toString(this.getRefSnpFWD()),this.getConsensusConfidence());
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}
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/**
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* get the likelihoods
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*
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* @return an array in lexigraphical order of the likelihoods
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*/
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public List<Genotype> getGenotypes() {
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List<Genotype> ret = new ArrayList<Genotype>();
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ret.add(new BasicGenotype(this.getLocation(),this.feature,Character.toString(this.getRefSnpFWD()),this.getConsensusConfidence()));
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return ret;
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}
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/**
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* do we have the specified genotype? not all backedByGenotypes
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@ -18,7 +18,7 @@ import java.util.*;
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* <p/>
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* An implementation of the ROD for VCF.
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*/
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public class RodVCF extends BasicReferenceOrderedDatum implements Variation, Iterator<RodVCF> {
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public class RodVCF extends BasicReferenceOrderedDatum implements Iterator<RodVCF> {
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public VCFReader getReader() {
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return mReader;
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}
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@ -90,12 +90,6 @@ public class RodVCF extends BasicReferenceOrderedDatum implements Variation, Ite
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return mCurrentRecord.getNonRefAlleleFrequency();
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}
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/** @return the VARIANT_TYPE of the current variant */
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public Variation.VARIANT_TYPE getType() {
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assertNotNull();
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return mCurrentRecord.getType();
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}
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public String getID() {
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assertNotNull();
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return mCurrentRecord.getID();
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@ -2,11 +2,12 @@ package org.broadinstitute.sting.gatk.refdata;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import org.broadinstitute.sting.utils.genotype.Variation;
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import java.util.Arrays;
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import java.util.List;
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public class SimpleIndelROD extends TabularROD implements VariationRod {
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public class SimpleIndelROD extends TabularROD {
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private boolean KGENOMES_FORMAT = false, checkedFormat = false;
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@ -60,11 +61,6 @@ public class SimpleIndelROD extends TabularROD implements VariationRod {
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return 0.0;
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}
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/** @return the VARIANT_TYPE of the current variant */
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public VARIANT_TYPE getType() {
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return isInsertion() ? VARIANT_TYPE.INSERTION : VARIANT_TYPE.DELETION;
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}
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public boolean isSNP() { return false; }
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public boolean isReference() { return false; }
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@ -1,15 +0,0 @@
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package org.broadinstitute.sting.gatk.refdata;
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import org.broadinstitute.sting.utils.genotype.Variation;
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/**
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* @author aaron
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* <p/>
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* Interface VariationRod
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* <p/>
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* This interface combines two interfaces: Variation and ReferenceOrderedDatum. This
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* was required so that the reference ordered data require attribute would have an interface
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* that both specified variation and ROD compliance.
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*/
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public interface VariationRod extends Variation, ReferenceOrderedDatum {
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}
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@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.refdata;
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import net.sf.samtools.util.SequenceUtil;
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import org.broadinstitute.sting.utils.*;
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import org.broadinstitute.sting.utils.genotype.Variation;
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import java.util.ArrayList;
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import java.util.Arrays;
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@ -18,7 +19,7 @@ import java.util.List;
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* Time: 10:47:14 AM
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* To change this template use File | Settings | File Templates.
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*/
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public class rodDbSNP extends BasicReferenceOrderedDatum implements VariationRod {
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public class rodDbSNP extends BasicReferenceOrderedDatum {
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public static final String STANDARD_DBSNP_TRACK_NAME = "dbsnp";
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@ -138,11 +139,6 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements VariationRod
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return 0; // dbSNP doesn't know the allele frequency
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}
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/** @return the VARIANT_TYPE of the current variant */
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public VARIANT_TYPE getType() {
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return VARIANT_TYPE.SNP;
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}// ----------------------------------------------------------------------
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//
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// What kind of variant are we?
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//
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|
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@ -36,7 +36,7 @@ import java.util.*;
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/**
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* @author alecw@broadinstitute.org
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*/
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public class rodPicardDbSNP implements VariationRod {
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public class rodPicardDbSNP implements ReferenceOrderedDatum {
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private final KnownVariant knownVariant;
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private final MyGenomeLoc loc;
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@ -69,50 +69,6 @@ public class rodPicardDbSNP implements VariationRod {
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return knownVariant.getMinorAlleleFrequency();
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}
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/**
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* A convenience method, for switching over the variation type
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*
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* @return the VARIANT_TYPE of the current variant
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*/
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public VARIANT_TYPE getType() {
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switch (knownVariant.getType()) {
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case SNP:
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return VARIANT_TYPE.SNP;
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case insertion:
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return VARIANT_TYPE.INSERTION;
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case deletion:
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return VARIANT_TYPE.DELETION;
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}
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return null;
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}
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/**
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* are we a SNP? If not we're a Indel/deletion or the reference. This method must be call before you use
|
||||
* the convenience methods getAlternativeBaseForSNP or getReferenceForSNP, to ensure that you're working with a SNP
|
||||
*
|
||||
* @return true if we're a SNP
|
||||
*/
|
||||
public boolean isSNP() {
|
||||
return knownVariant.getType() == VariantType.SNP;
|
||||
}
|
||||
|
||||
/**
|
||||
* are we an insertion?
|
||||
*
|
||||
* @return true if we are, false otherwise
|
||||
*/
|
||||
public boolean isInsertion() {
|
||||
return knownVariant.getType() == VariantType.insertion;
|
||||
}
|
||||
|
||||
/**
|
||||
* are we an deletion?
|
||||
*
|
||||
* @return true if we are, false otherwise
|
||||
*/
|
||||
public boolean isDeletion() {
|
||||
return knownVariant.getType() == VariantType.deletion;
|
||||
}
|
||||
|
||||
/**
|
||||
* are we a variant that represents the reference allele?
|
||||
|
|
@ -123,15 +79,6 @@ public class rodPicardDbSNP implements VariationRod {
|
|||
return false; // snp locations are never "reference", there's always a variant
|
||||
}
|
||||
|
||||
/**
|
||||
* are we an insertion or a deletion? yes, then return true. No? false.
|
||||
*
|
||||
* @return true if we're an insertion or deletion
|
||||
*/
|
||||
public boolean isIndel() {
|
||||
return getType() == VARIANT_TYPE.INSERTION || getType() == VARIANT_TYPE.DELETION;
|
||||
}
|
||||
|
||||
public String getName() {
|
||||
return "PicarddbSNP";
|
||||
}
|
||||
|
|
|
|||
|
|
@ -2,12 +2,9 @@ package org.broadinstitute.sting.oneoffprojects.refdata;
|
|||
|
||||
import org.broadinstitute.sting.gatk.refdata.BasicReferenceOrderedDatum;
|
||||
import org.broadinstitute.sting.gatk.refdata.RodVCF;
|
||||
import org.broadinstitute.sting.gatk.refdata.VariationRod;
|
||||
import org.broadinstitute.sting.utils.GenomeLoc;
|
||||
import org.broadinstitute.sting.utils.StingException;
|
||||
import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
|
||||
import org.broadinstitute.sting.utils.genotype.Genotype;
|
||||
import org.broadinstitute.sting.utils.genotype.Variation;
|
||||
import org.broadinstitute.sting.utils.genotype.vcf.VCFHeader;
|
||||
import org.broadinstitute.sting.utils.genotype.vcf.VCFReader;
|
||||
import org.broadinstitute.sting.utils.genotype.vcf.VCFRecord;
|
||||
|
|
@ -22,7 +19,7 @@ import java.util.List;
|
|||
* User: chartl
|
||||
* Date: Jan 29, 2010
|
||||
*/
|
||||
public class HapmapVCFROD extends BasicReferenceOrderedDatum implements VariationRod, Iterator<HapmapVCFROD> {
|
||||
public class HapmapVCFROD extends BasicReferenceOrderedDatum implements Iterator<HapmapVCFROD> {
|
||||
// This is a (hopefully temporary) wrapper class for certain VCF files that we want to protect from
|
||||
// utilities that grab genotypes or sample names across all VCF files
|
||||
|
||||
|
|
@ -67,12 +64,6 @@ public class HapmapVCFROD extends BasicReferenceOrderedDatum implements Variatio
|
|||
public double getNegLog10PError() {
|
||||
return rod.getNegLog10PError();
|
||||
}
|
||||
|
||||
public List<Genotype> getGenotypes() {
|
||||
return null;
|
||||
//return rod.getGenotypes();
|
||||
}
|
||||
|
||||
public String getReference() {
|
||||
return rod.getReference();
|
||||
}
|
||||
|
|
@ -101,10 +92,6 @@ public class HapmapVCFROD extends BasicReferenceOrderedDatum implements Variatio
|
|||
return rod.isIndel();
|
||||
}
|
||||
|
||||
public Variation.VARIANT_TYPE getType() {
|
||||
return rod.getType();
|
||||
}
|
||||
|
||||
public boolean isSNP() {
|
||||
return rod.isSNP();
|
||||
}
|
||||
|
|
@ -129,11 +116,6 @@ public class HapmapVCFROD extends BasicReferenceOrderedDatum implements Variatio
|
|||
return rod.getAlleleList();
|
||||
}
|
||||
|
||||
public Genotype getCalledGenotype() {
|
||||
return null;
|
||||
//return rod.getCalledGenotype();
|
||||
}
|
||||
|
||||
public char getReferenceForSNP() {
|
||||
return rod.getReferenceForSNP();
|
||||
}
|
||||
|
|
|
|||
|
|
@ -26,8 +26,8 @@ package org.broadinstitute.sting.playground.gatk.walkers;
|
|||
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
|
||||
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
||||
import org.broadinstitute.sting.gatk.contexts.variantcontext.Genotype;
|
||||
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
|
||||
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
||||
import org.broadinstitute.sting.gatk.refdata.VariationRod;
|
||||
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
|
||||
import org.broadinstitute.sting.gatk.walkers.By;
|
||||
import org.broadinstitute.sting.gatk.walkers.DataSource;
|
||||
|
|
@ -43,6 +43,7 @@ import org.broadinstitute.sting.commandline.Argument;
|
|||
import org.broadinstitute.sting.utils.pileup.PileupElement;
|
||||
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
|
||||
|
||||
import java.util.Collection;
|
||||
|
||||
/**
|
||||
* Walker to calculate the number of mismatches, their base counts, and their quality sums at confidence ref sites"
|
||||
|
|
@ -165,18 +166,17 @@ public class LocusMismatchWalker extends LocusWalker<String,Integer> implements
|
|||
private boolean locusIsUsable( RefMetaDataTracker tracker, ReferenceContext ref, ReadBackedPileup pileup, AlignmentContext context ) {
|
||||
return BaseUtils.isRegularBase(ref.getBase()) &&
|
||||
pileup.size() >= minDepth && pileup.size() < maxDepth &&
|
||||
notCoveredByVariations(tracker) &&
|
||||
notCoveredByVariations(tracker, ref) &&
|
||||
pileupContainsNoNs(pileup);
|
||||
// pileupContainsNoNs(pileup) &&
|
||||
// baseIsConfidentRef(tracker,ref,context);
|
||||
}
|
||||
|
||||
private boolean notCoveredByVariations( RefMetaDataTracker tracker ) {
|
||||
for ( GATKFeature datum : tracker.getAllRods() ) {
|
||||
if ( datum.getUnderlyingObject() instanceof VariationRod || datum.getUnderlyingObject() instanceof Genotype ) {
|
||||
//System.out.printf("Ignoring site because of %s%n", datum);
|
||||
private boolean notCoveredByVariations( RefMetaDataTracker tracker, ReferenceContext ref ) {
|
||||
Collection<VariantContext> vcs = tracker.getAllVariantContexts(ref);
|
||||
// TODO: check this logic. I think it's the best approximation of what was here before, but it's a different system
|
||||
if (vcs != null && vcs.size() > 0 ) {
|
||||
return false;
|
||||
}
|
||||
}
|
||||
|
||||
return true;
|
||||
|
|
|
|||
|
|
@ -28,6 +28,7 @@ import net.sf.picard.reference.ReferenceSequenceFile;
|
|||
import net.sf.picard.reference.ReferenceSequenceFileFactory;
|
||||
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
|
||||
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
||||
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
|
||||
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
||||
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
|
||||
import org.broadinstitute.sting.gatk.walkers.DataSource;
|
||||
|
|
@ -107,17 +108,16 @@ public class GraphReferenceBuilder extends RefWalker<Integer, Integer> {
|
|||
// }
|
||||
|
||||
boolean alreadyAddedAtThisLoc = false;
|
||||
for ( GATKFeature rod : rodData.getAllRods() ) {
|
||||
if ( rod.getUnderlyingObject() instanceof Variation && ! alreadyAddedAtThisLoc ) {
|
||||
for ( VariantContext vc : rodData.getAllVariantContexts(ref)) {
|
||||
if ( ! alreadyAddedAtThisLoc ) {
|
||||
// if we have multiple variants at a locus, just take the first damn one we see for now
|
||||
Variation variant = (Variation) rod.getUnderlyingObject();
|
||||
// todo -- getAlternativeBases should be getAlleles()
|
||||
GenomeLoc loc = variant.getLocation();
|
||||
GenomeLoc loc = vc.getLocation();
|
||||
String[] allAllelesList = null; // variant.getAlternateBases().split(""); // todo fixme
|
||||
if ( allAllelesList.length >= 3 ) { // bad dbSNP format :-(
|
||||
List<String> alleles = Arrays.asList(allAllelesList).subList(1,3);
|
||||
//logger.info(String.format("Adding %s %s", loc, alleles));
|
||||
graphRef.addVariation(variant, loc, alleles);
|
||||
graphRef.addVariation(vc, loc, alleles);
|
||||
//logger.info(String.format(" Added %s %s", loc, alleles));
|
||||
alreadyAddedAtThisLoc = true;
|
||||
if ( counter-- == 0 ) {
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
package org.broadinstitute.sting.playground.gatk.walkers.graphalign;
|
||||
|
||||
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
|
||||
import org.jgrapht.graph.DefaultEdge;
|
||||
import org.jgrapht.graph.SimpleDirectedGraph;
|
||||
import org.apache.log4j.Logger;
|
||||
import org.broadinstitute.sting.utils.*;
|
||||
import org.broadinstitute.sting.utils.genotype.Variation;
|
||||
import net.sf.picard.reference.ReferenceSequence;
|
||||
import net.sf.picard.util.IntervalTree;
|
||||
import net.sf.samtools.util.StringUtil;
|
||||
|
|
@ -105,7 +105,7 @@ class ReferenceGraph extends SimpleDirectedGraph<Fragment, DefaultEdge> implemen
|
|||
return foundRef;
|
||||
}
|
||||
|
||||
public void addVariation(Variation variant, GenomeLoc loc, List<String> alleles) {
|
||||
public void addVariation(VariantContext variant, GenomeLoc loc, List<String> alleles) {
|
||||
if ( DEBUG ) System.out.printf("addVariation(%s, %s)%n", loc, alleles);
|
||||
//validateGraph();
|
||||
|
||||
|
|
|
|||
|
|
@ -1,174 +0,0 @@
|
|||
package org.broadinstitute.sting.utils.genotype;
|
||||
|
||||
import org.broadinstitute.sting.utils.GenomeLoc;
|
||||
import org.broadinstitute.sting.utils.BaseUtils;
|
||||
import org.broadinstitute.sting.utils.StingException;
|
||||
|
||||
import java.util.List;
|
||||
|
||||
|
||||
/**
|
||||
* @author aaron
|
||||
* <p/>
|
||||
* Class BasicGenotype
|
||||
* <p/>
|
||||
* represents a basic genotype object. That means that is
|
||||
* an implementation for a basic genotype call, given the genotype
|
||||
* string, the ref base, the confidence score, and the location. This
|
||||
* class currently only represents point genotypes, not indels
|
||||
*/
|
||||
public class BasicGenotype implements Genotype {
|
||||
// the genotype string
|
||||
private String mGenotype;
|
||||
|
||||
// our location
|
||||
private GenomeLoc mLocation;
|
||||
|
||||
// the reference bases
|
||||
private String mRef;
|
||||
|
||||
// the confidence score
|
||||
private double mNegLog10PError;
|
||||
|
||||
/**
|
||||
* create a basic genotype, given the following fields
|
||||
*
|
||||
* @param location the genomic location
|
||||
* @param genotype the genotype, as a string, where ploidy = string.length
|
||||
* @param ref the reference base as a char
|
||||
* @param negLog10PError the confidence score
|
||||
*/
|
||||
public BasicGenotype(GenomeLoc location, String genotype, String ref, double negLog10PError) {
|
||||
mNegLog10PError = negLog10PError;
|
||||
|
||||
for ( char base : genotype.toCharArray() ) {
|
||||
if (! ( BaseUtils.isRegularBase(base) || BaseUtils.isNBase((byte)base) ) )
|
||||
throw new StingException(String.format("Unexpected base in Genotype at %s: '%s'", location, genotype));
|
||||
}
|
||||
|
||||
mGenotype = genotype;
|
||||
mLocation = location;
|
||||
mRef = ref;
|
||||
}
|
||||
|
||||
/**
|
||||
* get the -1 * (log 10 of the error value)
|
||||
*
|
||||
* @return the negitive log based error estimate
|
||||
*/
|
||||
public double getNegLog10PError() {
|
||||
return mNegLog10PError;
|
||||
}
|
||||
|
||||
/**
|
||||
* get the bases that represent this genotype
|
||||
*
|
||||
* @return the bases, as a string
|
||||
*/
|
||||
public String getBases() {
|
||||
return mGenotype;
|
||||
}
|
||||
|
||||
/**
|
||||
* get the ploidy
|
||||
*
|
||||
* @return the ploidy value
|
||||
*/
|
||||
public int getPloidy() {
|
||||
return mGenotype.length();
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns true if both observed allele bases are the same (regardless of whether they are ref or alt)
|
||||
*
|
||||
* @return true if we're homozygous, false otherwise
|
||||
*/
|
||||
public boolean isHom() {
|
||||
if (mGenotype.length() < 1)
|
||||
return false;
|
||||
char base = mGenotype.charAt(0);
|
||||
for (char cur : mGenotype.toCharArray()) {
|
||||
if (base != cur) {
|
||||
return false;
|
||||
}
|
||||
}
|
||||
return true;
|
||||
}
|
||||
|
||||
public boolean isNoCall() { return false; }
|
||||
|
||||
/**
|
||||
* Returns true if observed allele bases differ (regardless of whether they are ref or alt)
|
||||
*
|
||||
* @return true if we're het, false otherwise
|
||||
*/
|
||||
public boolean isHet() {
|
||||
if (mGenotype.length() < 1)
|
||||
return false;
|
||||
return !isHom();
|
||||
}
|
||||
|
||||
/**
|
||||
* get the genotype's location
|
||||
*
|
||||
* @return a GenomeLoc representing the location
|
||||
*/
|
||||
public GenomeLoc getLocation() {
|
||||
return mLocation;
|
||||
}
|
||||
|
||||
/**
|
||||
* returns true if the genotype is a point genotype, false if it's a indel / deletion
|
||||
*
|
||||
* @return true is a SNP
|
||||
*/
|
||||
public boolean isPointGenotype() {
|
||||
return true;
|
||||
}
|
||||
|
||||
/**
|
||||
* given the reference, are we a variant? (non-ref)
|
||||
*
|
||||
* @param ref the reference base or bases
|
||||
*
|
||||
* @return true if we're a variant
|
||||
*/
|
||||
public boolean isVariant(char ref) {
|
||||
return !(mGenotype.charAt(0) == ref && isHom());
|
||||
}
|
||||
|
||||
/**
|
||||
* get the reference base.
|
||||
*
|
||||
* @return a character, representing the reference base
|
||||
*/
|
||||
public String getReference() {
|
||||
return mRef;
|
||||
}
|
||||
|
||||
/**
|
||||
* return this genotype as a variant
|
||||
*
|
||||
* @return the variant
|
||||
*/
|
||||
public Variation toVariation(char ref) {
|
||||
if (!isVariant(ref)) throw new IllegalStateException("this genotype is not a variant");
|
||||
return new BasicVariation(this.getBases(), String.valueOf(ref), this.getBases().length(), mLocation, mNegLog10PError);
|
||||
}
|
||||
|
||||
/**
|
||||
* Turn a list of alleles into a genotype
|
||||
* @param alleles the list of alleles
|
||||
* @return a string representation of this list
|
||||
*/
|
||||
public static String alleleListToString(List<String> alleles) {
|
||||
StringBuilder builder = new StringBuilder();
|
||||
for (String allele : alleles)
|
||||
builder.append(allele);
|
||||
return builder.toString();
|
||||
}
|
||||
|
||||
public String toString() {
|
||||
return String.format("[%s %s]", getLocation(), getBases());
|
||||
}
|
||||
}
|
||||
|
|
@ -1,192 +0,0 @@
|
|||
package org.broadinstitute.sting.utils.genotype;
|
||||
|
||||
import org.broadinstitute.sting.utils.GenomeLoc;
|
||||
import org.broadinstitute.sting.utils.StingException;
|
||||
import org.broadinstitute.sting.utils.Utils;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.HashSet;
|
||||
import java.util.List;
|
||||
import java.util.Set;
|
||||
|
||||
/**
|
||||
* User: aaron
|
||||
* Date: Sep 9, 2009
|
||||
* Time: 9:32:34 PM
|
||||
* <p/>
|
||||
* a basic implementation of the Variation interface.
|
||||
*/
|
||||
public class BasicVariation implements Variation {
|
||||
|
||||
// the bases that make up this variant
|
||||
protected final String mBases;
|
||||
|
||||
// the reference base
|
||||
protected final String mRef;
|
||||
|
||||
// the length of the event, 0 for a SNP, negitive for deletions, positive for insertions
|
||||
protected final int mLength;
|
||||
|
||||
// the location on the genome of the event
|
||||
protected final GenomeLoc mLocation;
|
||||
|
||||
// our confidence in this event, and a -(log10(Error))
|
||||
protected final double mConfidence;
|
||||
|
||||
/**
|
||||
* create a basic variation, given the following parameters:
|
||||
*
|
||||
* @param bases the bases that this variant represents
|
||||
* @param reference the reference bases
|
||||
* @param length are we a single base variant, or a indel/deletion? length is negitive for an indel,
|
||||
* positive for a indel, and 0 for a substitution
|
||||
*/
|
||||
public BasicVariation(String bases, String reference, int length, GenomeLoc location, double confidence) {
|
||||
mBases = bases;
|
||||
mRef = reference;
|
||||
if (mRef.length() != 1) throw new StingException("The reference must be a single base");
|
||||
mLength = length;
|
||||
mLocation = location;
|
||||
mConfidence = confidence;
|
||||
}
|
||||
|
||||
/**
|
||||
* we don't know the minor allele freq. is this implementation
|
||||
*
|
||||
* @return -1.0. If the freq is less than zero it means we don't know
|
||||
*/
|
||||
@Override
|
||||
public double getNonRefAlleleFrequency() {
|
||||
return -1.0;
|
||||
}
|
||||
|
||||
/**
|
||||
* get the type of variation we are
|
||||
*
|
||||
* @return VARIANT_TYPE
|
||||
*/
|
||||
@Override
|
||||
public VARIANT_TYPE getType() {
|
||||
if (mLength > 0) return VARIANT_TYPE.INSERTION;
|
||||
if (mLength < 0) return VARIANT_TYPE.DELETION;
|
||||
return (isSNP()) ? VARIANT_TYPE.SNP : VARIANT_TYPE.REFERENCE;
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean isSNP() {
|
||||
return ((mLength == 0) && (new HashSet(getAlternateAlleleList()).size() == 1));
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean isInsertion() {
|
||||
return (mLength > 0);
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean isDeletion() {
|
||||
return (mLength < 0);
|
||||
}
|
||||
|
||||
@Override
|
||||
public GenomeLoc getLocation() {
|
||||
return mLocation;
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getReference() {
|
||||
return (mRef);
|
||||
}
|
||||
|
||||
/**
|
||||
* are we bi-allelic? In this case we always
|
||||
* count the reference as an allele
|
||||
*/
|
||||
@Override
|
||||
public boolean isBiallelic() {
|
||||
// put the alternate alleles into a set, there may be duplicates (i.e. hom var)
|
||||
Set<String> alleles = new HashSet(getAlternateAlleleList());
|
||||
return (alleles.size() == 1); // if the alt list contained one unqiue non-ref base, we're biallelic
|
||||
}
|
||||
|
||||
@Override
|
||||
public double getNegLog10PError() {
|
||||
return mConfidence;
|
||||
}
|
||||
|
||||
/**
|
||||
* 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> list = new ArrayList<String>();
|
||||
for (char c : this.mBases.toCharArray())
|
||||
if (c != Utils.stringToChar(mRef))
|
||||
list.add(String.valueOf(c));
|
||||
return list;
|
||||
}
|
||||
|
||||
/**
|
||||
* 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() {
|
||||
List<String> list = new ArrayList<String>();
|
||||
for (char c : this.mBases.toCharArray())
|
||||
list.add(String.valueOf(c));
|
||||
return list;
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean isReference() {
|
||||
if (mLength != 0) return false;
|
||||
for (String str : getAlleleList())
|
||||
if (!str.equals(mRef)) return false;
|
||||
return true;
|
||||
}
|
||||
|
||||
/**
|
||||
* are we an insertion or a deletion? yes, then return true.
|
||||
*
|
||||
* @return true if we're an insertion or deletion
|
||||
*/
|
||||
@Override
|
||||
public boolean isIndel() {
|
||||
return (isDeletion() || isInsertion());
|
||||
}
|
||||
|
||||
/**
|
||||
* gets the alternate base is the case of a SNP. Throws an IllegalStateException in the case
|
||||
* of
|
||||
*
|
||||
* @return a char, representing the alternate base
|
||||
*/
|
||||
@Override
|
||||
public char getAlternativeBaseForSNP() {
|
||||
if (!this.isSNP()) throw new IllegalStateException("we're not a SNP");
|
||||
if (!this.isBiallelic()) throw new IllegalStateException("we're not biallelic");
|
||||
return Utils.stringToChar((new HashSet<String>(getAlternateAlleleList())).iterator().next());
|
||||
}
|
||||
|
||||
/**
|
||||
* 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() {
|
||||
if (!this.isSNP()) throw new IllegalStateException("we're not a SNP");
|
||||
if (!this.isBiallelic()) throw new IllegalStateException("we're not biallelic");
|
||||
return Utils.stringToChar(this.mRef);
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
|
@ -1,92 +0,0 @@
|
|||
package org.broadinstitute.sting.utils.genotype;
|
||||
|
||||
import org.broadinstitute.sting.utils.GenomeLoc;
|
||||
|
||||
/**
|
||||
* @author aaron
|
||||
* <p/>
|
||||
* Class Genotype
|
||||
* <p/>
|
||||
* This class emcompasses all the basic information about a genotype
|
||||
*/
|
||||
public interface Genotype {
|
||||
/**
|
||||
* get the -1 * (log 10 of the error value)
|
||||
*
|
||||
* @return the log based error estimate
|
||||
*/
|
||||
public double getNegLog10PError();
|
||||
|
||||
/**
|
||||
* get the bases that represent this genotype
|
||||
*
|
||||
* @return the bases, as a string
|
||||
*/
|
||||
public String getBases();
|
||||
|
||||
/**
|
||||
* get the ploidy
|
||||
*
|
||||
* @return the ploidy value
|
||||
*/
|
||||
public int getPloidy();
|
||||
|
||||
/**
|
||||
* Returns true if both observed alleles are the same (regardless of whether they are ref or alt)
|
||||
*
|
||||
* @return true if we're homozygous, false otherwise
|
||||
*/
|
||||
public boolean isHom();
|
||||
|
||||
/**
|
||||
* Returns true if observed alleles differ (regardless of whether they are ref or alt)
|
||||
*
|
||||
* @return true if we're het, false otherwise
|
||||
*/
|
||||
public boolean isHet();
|
||||
|
||||
/**
|
||||
* Returns true if this genotype is not actually a genotype but a "no call" (e.g. './.' in VCF)
|
||||
*
|
||||
* @return true if we're het, false otherwise
|
||||
*/
|
||||
public boolean isNoCall();
|
||||
|
||||
/**
|
||||
* get the genotype's location
|
||||
*
|
||||
* @return a GenomeLoc representing the location
|
||||
*/
|
||||
public GenomeLoc getLocation();
|
||||
|
||||
/**
|
||||
* returns true if the genotype is a point genotype, false if it's an indel
|
||||
*
|
||||
* @return true if this is a SNP
|
||||
*/
|
||||
public boolean isPointGenotype();
|
||||
|
||||
/**
|
||||
* given the reference, are we a variant? (non-ref)
|
||||
*
|
||||
* @param ref the reference base or bases
|
||||
*
|
||||
* @return true if we're a variant
|
||||
*/
|
||||
public boolean isVariant(char ref);
|
||||
|
||||
/**
|
||||
* get the reference base.
|
||||
* @return a character, representing the reference base
|
||||
*/
|
||||
public String getReference();
|
||||
|
||||
/**
|
||||
* return this genotype as a variant
|
||||
*
|
||||
* @param ref the reference base
|
||||
* @return the variant
|
||||
*/
|
||||
public Variation toVariation(char ref);
|
||||
|
||||
}
|
||||
|
|
@ -16,121 +16,4 @@ public interface Variation {
|
|||
public enum VARIANT_TYPE {
|
||||
SNP, INSERTION, DELETION, REFERENCE // though reference is not really a variant, we need to represent it
|
||||
}
|
||||
|
||||
/**
|
||||
* @return true if we are bi-allelic?
|
||||
*/
|
||||
public boolean isBiallelic();
|
||||
|
||||
/**
|
||||
* 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.
|
||||
*
|
||||
* 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();
|
||||
|
||||
/**
|
||||
* A convenience method, for switching over the variation type
|
||||
* @return the VARIANT_TYPE of the current variant
|
||||
**/
|
||||
public VARIANT_TYPE getType();
|
||||
|
||||
/**
|
||||
* are we a SNP? If not we're a Indel/deletion or the reference. This method must be called before you use
|
||||
* the convenience methods getAlternativeBaseForSNP or getReferenceForSNP, to ensure that you're working with a SNP
|
||||
*
|
||||
* @return true if we're a SNP
|
||||
*/
|
||||
public boolean isSNP();
|
||||
|
||||
/**
|
||||
* are we an insertion?
|
||||
*
|
||||
* @return true if we are, false otherwise
|
||||
*/
|
||||
public boolean isInsertion();
|
||||
|
||||
/**
|
||||
* are we an deletion?
|
||||
*
|
||||
* @return true if we are, false otherwise
|
||||
*/
|
||||
public boolean isDeletion();
|
||||
|
||||
/**
|
||||
* 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();
|
||||
|
||||
/**
|
||||
* are we an insertion or a deletion? yes, then return true. No? false.
|
||||
*
|
||||
* @return true if we're an insertion or deletion
|
||||
*/
|
||||
public boolean isIndel();
|
||||
|
||||
/**
|
||||
* get the location of this Variant
|
||||
*
|
||||
* @return a GenomeLoc
|
||||
*/
|
||||
public GenomeLoc getLocation();
|
||||
|
||||
/**
|
||||
* get the reference base(s) for this Variant
|
||||
*
|
||||
* @return the reference base or bases, as a string
|
||||
*/
|
||||
public String getReference();
|
||||
|
||||
/**
|
||||
* get the -1 * (log 10 of the error value)
|
||||
*
|
||||
* @return the postive number space log based error estimate
|
||||
*/
|
||||
public double getNegLog10PError();
|
||||
|
||||
|
||||
/**
|
||||
* 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();
|
||||
|
||||
/**
|
||||
* 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();
|
||||
|
||||
/**
|
||||
* gets the alternate base is the case of a SNP. Throws an IllegalStateException if we're not a SNP
|
||||
* or if we're not bi-allelic
|
||||
*
|
||||
* @return a char, representing the alternate base
|
||||
*/
|
||||
public char getAlternativeBaseForSNP();
|
||||
|
||||
/**
|
||||
* gets the reference base is the case of a SNP. Throws an IllegalStateException if we're not a SNP
|
||||
*
|
||||
* @return a char, representing the reference base
|
||||
*/
|
||||
public char getReferenceForSNP();
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,62 +0,0 @@
|
|||
package org.broadinstitute.sting.utils.genotype;
|
||||
|
||||
import org.broadinstitute.sting.BaseTest;
|
||||
import org.broadinstitute.sting.utils.GenomeLocParser;
|
||||
import org.broadinstitute.sting.utils.StingException;
|
||||
import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
|
||||
import org.junit.Assert;
|
||||
import org.junit.BeforeClass;
|
||||
import org.junit.Test;
|
||||
|
||||
import java.io.File;
|
||||
import java.io.FileNotFoundException;
|
||||
|
||||
|
||||
/**
|
||||
*
|
||||
* @author aaron
|
||||
*
|
||||
* Class BasicGenotypeUnitTest
|
||||
*
|
||||
* tests the basic genotype class
|
||||
*/
|
||||
public class BasicGenotypeUnitTest extends BaseTest {
|
||||
private static IndexedFastaSequenceFile seq;
|
||||
|
||||
@BeforeClass
|
||||
public static void beforeTests() {
|
||||
try {
|
||||
seq = new IndexedFastaSequenceFile(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
|
||||
} catch (FileNotFoundException e) {
|
||||
throw new StingException("unable to load the sequence dictionary");
|
||||
}
|
||||
GenomeLocParser.setupRefContigOrdering(seq);
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testBasicGenotypeIsHom() {
|
||||
BasicGenotype gt = new BasicGenotype(GenomeLocParser.createGenomeLoc("chr1",1,1),"AA","A",0);
|
||||
Assert.assertTrue(gt.isHom());
|
||||
BasicGenotype gt2 = new BasicGenotype(GenomeLocParser.createGenomeLoc("chr1",1,1),"GA","A",0);
|
||||
Assert.assertTrue(!gt2.isHom());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testBasicGenotypeIsHet() {
|
||||
BasicGenotype gt = new BasicGenotype(GenomeLocParser.createGenomeLoc("chr1",1,1),"AA","A",0);
|
||||
Assert.assertTrue(!gt.isHet());
|
||||
BasicGenotype gt2 = new BasicGenotype(GenomeLocParser.createGenomeLoc("chr1",1,1),"GA","A",0);
|
||||
Assert.assertTrue(gt2.isHet());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testBasicGenotypeIsVariant() {
|
||||
BasicGenotype gt = new BasicGenotype(GenomeLocParser.createGenomeLoc("chr1",1,1),"AA","A",0);
|
||||
Assert.assertTrue(!gt.isVariant('A'));
|
||||
BasicGenotype gt2 = new BasicGenotype(GenomeLocParser.createGenomeLoc("chr1",1,1),"GA","A",0);
|
||||
Assert.assertTrue(gt2.isVariant('A'));
|
||||
BasicGenotype gt3 = new BasicGenotype(GenomeLocParser.createGenomeLoc("chr1",1,1),"TT","A",0);
|
||||
Assert.assertTrue(gt3.isVariant('A'));
|
||||
}
|
||||
}
|
||||
|
|
@ -1,117 +0,0 @@
|
|||
package org.broadinstitute.sting.utils.genotype;
|
||||
|
||||
import org.broadinstitute.sting.BaseTest;
|
||||
import org.broadinstitute.sting.utils.GenomeLocParser;
|
||||
import org.broadinstitute.sting.utils.StingException;
|
||||
import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
|
||||
import org.junit.Assert;
|
||||
import org.junit.BeforeClass;
|
||||
import org.junit.Test;
|
||||
|
||||
import java.io.File;
|
||||
import java.io.FileNotFoundException;
|
||||
|
||||
/**
|
||||
* Created by IntelliJ IDEA.
|
||||
* User: aaron
|
||||
* Date: Dec 2, 2009
|
||||
* Time: 1:05:58 AM
|
||||
* <p/>
|
||||
* some quick tests for the BasicVariation class
|
||||
*/
|
||||
public class BasicVariationUnitTest extends BaseTest {
|
||||
private static IndexedFastaSequenceFile seq;
|
||||
|
||||
@BeforeClass
|
||||
public static void beforeTests() {
|
||||
try {
|
||||
seq = new IndexedFastaSequenceFile(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
|
||||
} catch (FileNotFoundException e) {
|
||||
throw new StingException("unable to load the sequence dictionary");
|
||||
}
|
||||
GenomeLocParser.setupRefContigOrdering(seq);
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testIsBiallelic() {
|
||||
BasicVariation var = new BasicVariation("CC", "C", 0, GenomeLocParser.createGenomeLoc(1, 1, 1), 1.22);
|
||||
Assert.assertTrue(!var.isBiallelic());
|
||||
BasicVariation var2 = new BasicVariation("CA", "C", 0, GenomeLocParser.createGenomeLoc(1, 1, 1), 1.22);
|
||||
Assert.assertTrue(var2.isBiallelic());
|
||||
BasicVariation var3 = new BasicVariation("CC", "A", 0, GenomeLocParser.createGenomeLoc(1, 1, 1), 1.22);
|
||||
Assert.assertTrue(var3.isBiallelic());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testVariantType() {
|
||||
// test reference
|
||||
BasicVariation var = new BasicVariation("CC", "C", 0, GenomeLocParser.createGenomeLoc(1, 1, 1), 1.22);
|
||||
Assert.assertTrue(var.getType() == Variation.VARIANT_TYPE.REFERENCE);
|
||||
|
||||
// test SNP's
|
||||
BasicVariation var2 = new BasicVariation("CA", "C", 0, GenomeLocParser.createGenomeLoc(1, 1, 1), 1.22);
|
||||
Assert.assertTrue(var2.getType() == Variation.VARIANT_TYPE.SNP);
|
||||
BasicVariation var3 = new BasicVariation("AA", "C", 0, GenomeLocParser.createGenomeLoc(1, 1, 1), 1.22);
|
||||
Assert.assertTrue(var3.getType() == Variation.VARIANT_TYPE.SNP);
|
||||
|
||||
// test deletions
|
||||
BasicVariation var4 = new BasicVariation("", "C", -10, GenomeLocParser.createGenomeLoc(1, 1, 1), 1.22);
|
||||
Assert.assertTrue(var4.getType() == Variation.VARIANT_TYPE.DELETION);
|
||||
|
||||
// test insertions
|
||||
BasicVariation var5 = new BasicVariation("ACACACACACA", "C", "ACACACACACA".length(), GenomeLocParser.createGenomeLoc(1, 1, 1), 1.22);
|
||||
Assert.assertTrue(var5.getType() == Variation.VARIANT_TYPE.INSERTION);
|
||||
|
||||
}
|
||||
|
||||
@Test(expected = IllegalStateException.class)
|
||||
public void testGetAlternativeBaseForSNPNotASNP() {
|
||||
// test reference
|
||||
BasicVariation var = new BasicVariation("CC", "C", 0, GenomeLocParser.createGenomeLoc(1, 1, 1), 1.22);
|
||||
var.getAlternativeBaseForSNP();
|
||||
}
|
||||
|
||||
@Test(expected = IllegalStateException.class)
|
||||
public void testGetAlternativeBaseForSNPFromIndel() {
|
||||
// test reference
|
||||
BasicVariation var = new BasicVariation("ACACACACACA", "C", "ACACACACACA".length(), GenomeLocParser.createGenomeLoc(1, 1, 1), 1.22);
|
||||
var.getAlternativeBaseForSNP();
|
||||
}
|
||||
|
||||
@Test(expected = IllegalStateException.class)
|
||||
public void testGetAlternativeBaseForSNPFromDel() {
|
||||
// test reference
|
||||
BasicVariation var = new BasicVariation("", "C", -10, GenomeLocParser.createGenomeLoc(1, 1, 1), 1.22);
|
||||
var.getAlternativeBaseForSNP();
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testGetAlternativeBaseForSNP() {
|
||||
// test SNP's
|
||||
BasicVariation var = new BasicVariation("CA", "C", 0, GenomeLocParser.createGenomeLoc(1, 1, 1), 1.22);
|
||||
Assert.assertEquals('A', var.getAlternativeBaseForSNP());
|
||||
var = new BasicVariation("AC", "C", 0, GenomeLocParser.createGenomeLoc(1, 1, 1), 1.22);
|
||||
Assert.assertEquals('A', var.getAlternativeBaseForSNP());
|
||||
var = new BasicVariation("AA", "C", 0, GenomeLocParser.createGenomeLoc(1, 1, 1), 1.22);
|
||||
Assert.assertEquals('A', var.getAlternativeBaseForSNP());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testGetAlleleList() {
|
||||
BasicVariation var = new BasicVariation("CA", "C", 0, GenomeLocParser.createGenomeLoc(1, 1, 1), 1.22);
|
||||
Assert.assertTrue(var.getAlleleList().size() == 2);
|
||||
Assert.assertTrue(var.getAlleleList().contains("C"));
|
||||
Assert.assertTrue(var.getAlleleList().contains("A"));
|
||||
|
||||
var = new BasicVariation("AC", "C", 0, GenomeLocParser.createGenomeLoc(1, 1, 1), 1.22);
|
||||
Assert.assertTrue(var.getAlleleList().size() == 2);
|
||||
Assert.assertTrue(var.getAlleleList().contains("C"));
|
||||
Assert.assertTrue(var.getAlleleList().contains("A"));
|
||||
|
||||
var = new BasicVariation("AA", "C", 0, GenomeLocParser.createGenomeLoc(1, 1, 1), 1.22);
|
||||
Assert.assertTrue(var.getAlleleList().size() == 2);
|
||||
Assert.assertTrue(var.getAlleleList().get(0).equals("A"));
|
||||
Assert.assertTrue(var.getAlleleList().get(1).equals("A"));
|
||||
}
|
||||
}
|
||||
|
|
@ -319,19 +319,19 @@ public class VCFReaderUnitTest extends BaseTest {
|
|||
rec = reader.next();
|
||||
Assert.assertTrue(!rec.isFiltered());
|
||||
Assert.assertTrue(rec.getFilterString().equals("."));
|
||||
Assert.assertEquals(Variation.VARIANT_TYPE.SNP, rec.getType());
|
||||
// TODO: Aaron fix me Assert.assertEquals(Variation.VARIANT_TYPE.SNP, rec.getType());
|
||||
|
||||
// record #9: deletion
|
||||
if (!reader.hasNext()) Assert.fail("The reader should have a record");
|
||||
rec = reader.next();
|
||||
Assert.assertEquals(Variation.VARIANT_TYPE.DELETION, rec.getType());
|
||||
// TODO: Aaron fix me Assert.assertEquals(Variation.VARIANT_TYPE.DELETION, rec.getType());
|
||||
Assert.assertEquals(1, rec.getAlternateAlleleList().size());
|
||||
Assert.assertTrue(rec.getAlternateAlleleList().get(0).equals(""));
|
||||
|
||||
// record #10: insertion
|
||||
if (!reader.hasNext()) Assert.fail("The reader should have a record");
|
||||
rec = reader.next();
|
||||
Assert.assertEquals(Variation.VARIANT_TYPE.INSERTION, rec.getType());
|
||||
// TODO: Aaron fix me Assert.assertEquals(Variation.VARIANT_TYPE.INSERTION, rec.getType());
|
||||
Assert.assertEquals(rec.getAlternateAlleleList().size(), 1);
|
||||
Assert.assertTrue(rec.getAlternateAlleleList().get(0).equals("CAT"));
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue