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Trying to restore SVN history for phasing directory 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4371 348d0f76-0448-11de-a6fe-93d51630548a
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fromer 2010-09-28 23:48:24 +00:00
parent dfb5143a41
commit bf88117ead
3 changed files with 0 additions and 1796 deletions
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72
java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
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@ -1,72 +0,0 @@
/*
* Copyright (c) 2010, 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.walkers.phasing;
import org.broad.tribble.util.variantcontext.Allele;
import org.broad.tribble.util.variantcontext.Genotype;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.ArrayList;
import java.util.List;
public class AllelePair {
private Allele top;
private Allele bottom;
public AllelePair(Genotype gt) {
if (gt.getPloidy() != 2)
throw new ReviewedStingException("AllelePair must have ploidy of 2!");
this.top = gt.getAllele(0);
this.bottom = gt.getAllele(1);
}
public Allele getTopAllele() {
return top;
}
public Allele getBottomAllele() {
return bottom;
}
public void swapAlleles() {
Allele tmp = top;
top = bottom;
bottom = tmp;
}
public List<Allele> getAllelesAsList() {
List<Allele> allList = new ArrayList<Allele>(2);
allList.add(0, top);
allList.add(1, bottom);
return allList;
}
public String toString() {
StringBuilder sb = new StringBuilder();
sb.append("Top:\t" + top.getBaseString() + "\n");
sb.append("Bot:\t" + bottom.getBaseString() + "\n");
return sb.toString();
}
}

1649
java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
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75
java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java
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@ -1,75 +0,0 @@
/*
* Copyright (c) 2010, 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.walkers.phasing;
import org.broad.tribble.util.variantcontext.Allele;
import org.broad.tribble.util.variantcontext.Genotype;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
public class SNPallelePair extends AllelePair {
public SNPallelePair(Genotype gt) {
super(gt);
if (getTopAllele().getBases().length != 1)
throw new ReviewedStingException("LOGICAL ERROR: SNPallelePair may not contain non-SNP site!");
if (getBottomAllele().getBases().length != 1)
throw new ReviewedStingException("LOGICAL ERROR: SNPallelePair may not contain non-SNP site!");
}
public byte getTopBase() {
byte[] topBases = getTopAllele().getBases();
return getSingleBase(topBases);
}
public byte getBottomBase() {
byte[] bottomBases = getBottomAllele().getBases();
return getSingleBase(bottomBases);
}
public boolean matchesTopBase(byte base) {
return BaseUtils.basesAreEqual(base, getTopBase());
}
public byte getOtherBase(byte base) {
byte topBase = getTopBase();
byte botBase = getBottomBase();
if (BaseUtils.basesAreEqual(base, topBase))
return botBase;
else if (BaseUtils.basesAreEqual(base, botBase))
return topBase;
else
throw new ReviewedStingException("LOGICAL ERROR: base MUST match either TOP or BOTTOM!");
}
public static byte getSingleBase(byte[] bases) {
return bases[0];
}
public static byte getSingleBase(Allele all) {
return getSingleBase(all.getBases());
}
}