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Hacks for getting GLFs support in the Rod system working 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1268 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-07-16 21:03:47 +00:00
parent 0548026a2e
commit 107f42a01e
4 changed files with 37 additions and 31 deletions
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25
java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
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@ -1,21 +1,18 @@
package org.broadinstitute.sting.gatk.refdata; package org.broadinstitute.sting.gatk.refdata;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.MalformedGenomeLocException;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.xReadLines;
import java.io.File; import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileWriter; import java.io.FileWriter;
import java.io.IOException; import java.io.IOException;
import java.io.FileNotFoundException;
import java.util.*;
import java.lang.reflect.Constructor; import java.lang.reflect.Constructor;
import java.lang.reflect.InvocationTargetException; import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method; import java.lang.reflect.Method;
import java.util.*;
import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
import org.broadinstitute.sting.gatk.refdata.rodRefSeq;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.xReadLines;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.MalformedGenomeLocException;
import org.apache.log4j.Logger;
/** /**
* Class for representing arbitrary reference ordered data sets * Class for representing arbitrary reference ordered data sets
@ -53,8 +50,12 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
public static HashMap<String, RODBinding> Types = new HashMap<String, RODBinding>(); public static HashMap<String, RODBinding> Types = new HashMap<String, RODBinding>();
public static void addModule(final String name, final Class<? extends ReferenceOrderedDatum> rodType) { public static void addModule(final String name, final Class<? extends ReferenceOrderedDatum> rodType) {
final String boundName = name.toLowerCase();
if ( Types.containsKey(boundName) ) {
throw new RuntimeException(String.format("GATK BUG: adding ROD module %s that is already bound", boundName));
}
System.out.printf("* Adding rod class %s%n", name); System.out.printf("* Adding rod class %s%n", name);
Types.put(name.toLowerCase(), new RODBinding(name, rodType)); Types.put(boundName, new RODBinding(name, rodType));
} }
static { static {
@ -64,7 +65,6 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
addModule("HapMapAlleleFrequencies", HapMapAlleleFrequenciesROD.class); addModule("HapMapAlleleFrequencies", HapMapAlleleFrequenciesROD.class);
addModule("SAMPileup", rodSAMPileup.class); addModule("SAMPileup", rodSAMPileup.class);
addModule("GELI", rodGELI.class); addModule("GELI", rodGELI.class);
addModule("FLT", rodFLT.class);
addModule("RefSeq", rodRefSeq.class); addModule("RefSeq", rodRefSeq.class);
addModule("Table", TabularROD.class); addModule("Table", TabularROD.class);
addModule("PooledEM", PooledEMSNPROD.class); addModule("PooledEM", PooledEMSNPROD.class);
@ -73,6 +73,7 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
addModule("HapMapGenotype", HapMapGenotypeROD.class); addModule("HapMapGenotype", HapMapGenotypeROD.class);
addModule("Intervals", IntervalRod.class); addModule("Intervals", IntervalRod.class);
addModule("Variants", rodVariants.class); addModule("Variants", rodVariants.class);
addModule("GLF", RodGLF.class);
} }

2
java/src/org/broadinstitute/sting/gatk/refdata/RodGLF.java
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@ -20,7 +20,7 @@ import java.util.Iterator;
* the rod class for GLF data. * the rod class for GLF data.
*/ */
public class RodGLF extends BasicReferenceOrderedDatum { public class RodGLF extends BasicReferenceOrderedDatum {
protected GLFRecord mRecord; public GLFRecord mRecord;
private GenomeLoc mLoc; private GenomeLoc mLoc;
private static GLFRODIterator mWrap; private static GLFRODIterator mWrap;
private String contig; private String contig;

35
java/src/org/broadinstitute/sting/gatk/refdata/rodVariants.java
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@ -33,16 +33,15 @@ import java.util.Arrays;
*/ */
public class rodVariants extends BasicReferenceOrderedDatum implements AllelicVariant { public class rodVariants extends BasicReferenceOrderedDatum implements AllelicVariant {
private enum Genotype { AA, AC, AG, AT, CC, CG, CT, GG, GT, TT } public enum Genotype { AA, AC, AG, AT, CC, CG, CT, GG, GT, TT }
public GenomeLoc loc;
private GenomeLoc loc; public char refBase = 'N';
private char refBase = 'N'; public int depth;
private int depth; public int maxMappingQuality;
private int maxMappingQuality; public String bestGenotype = "NN";
private String bestGenotype = "NN"; public double lodBtr;
private float lodBtr; public double lodBtnb;
private float lodBtnb; public double[] genotypeLikelihoods = new double[10];
private float[] genotypeLikelihoods = new float[10];
public rodVariants(final String name) { super(name); } public rodVariants(final String name) { super(name); }
@ -55,11 +54,11 @@ public class rodVariants extends BasicReferenceOrderedDatum implements AllelicVa
depth = Integer.valueOf(parts[3]); depth = Integer.valueOf(parts[3]);
maxMappingQuality = Integer.valueOf(parts[4]); maxMappingQuality = Integer.valueOf(parts[4]);
bestGenotype = parts[5]; bestGenotype = parts[5];
lodBtr = Float.valueOf(parts[6]); lodBtr = Double.valueOf(parts[6]);
lodBtnb = Float.valueOf(parts[7]); lodBtnb = Double.valueOf(parts[7]);
for (int pieceIndex = 8, offset = 0; pieceIndex < 18; pieceIndex++, offset++) { for (int pieceIndex = 8, offset = 0; pieceIndex < 18; pieceIndex++, offset++) {
genotypeLikelihoods[offset] = Float.valueOf(parts[pieceIndex]); genotypeLikelihoods[offset] = Double.valueOf(parts[pieceIndex]);
} }
return true; return true;
@ -101,11 +100,11 @@ public class rodVariants extends BasicReferenceOrderedDatum implements AllelicVa
public String getBestGenotype() { return bestGenotype; } public String getBestGenotype() { return bestGenotype; }
public float getLodBtr() { return lodBtr; } public double getLodBtr() { return lodBtr; }
public float getLodBtnb() { return lodBtnb; } public double getLodBtnb() { return lodBtnb; }
public float[] getGenotypeLikelihoods() { return genotypeLikelihoods; } public double[] getGenotypeLikelihoods() { return genotypeLikelihoods; }
public void adjustLikelihoods(double[] likelihoods) { public void adjustLikelihoods(double[] likelihoods) {
for (int likelihoodIndex = 0; likelihoodIndex < likelihoods.length; likelihoodIndex++) { for (int likelihoodIndex = 0; likelihoodIndex < likelihoods.length; likelihoodIndex++) {
@ -139,8 +138,8 @@ public class rodVariants extends BasicReferenceOrderedDatum implements AllelicVa
} }
this.bestGenotype = bestGenotype; this.bestGenotype = bestGenotype;
this.lodBtr = (float) (bestLikelihood - refLikelihood); this.lodBtr = (bestLikelihood - refLikelihood);
this.lodBtnb = (float) (bestLikelihood - nextBestLikelihood); this.lodBtnb = (bestLikelihood - nextBestLikelihood);
} }
public String getRefBasesFWD() { public String getRefBasesFWD() {

6
java/src/org/broadinstitute/sting/utils/genotype/glf/GLFRecord.java
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@ -2,6 +2,10 @@ package org.broadinstitute.sting.utils.genotype.glf;
import net.sf.samtools.util.BinaryCodec; import net.sf.samtools.util.BinaryCodec;
import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.gatk.refdata.AllelicVariant;
import java.util.List;
import java.util.Arrays;
/* /*
@ -40,6 +44,8 @@ import org.broadinstitute.sting.utils.StingException;
* field values. * field values.
*/ */
public abstract class GLFRecord { public abstract class GLFRecord {
public final static double LIKELIHOOD_SCALE_FACTOR = 1;
// fields common to all records // fields common to all records
protected REF_BASE refBase; protected REF_BASE refBase;