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Remove no longer in use Eval modules from VariantEval 

-- No more IndelLengthHistogram (superceded by IndelSummary in subsequent commit)
-- No more SamplePreviousGenotypes or PhaseStats
-- No more MultiallelicAFs
This commit is contained in:
Mark DePristo 2012-03-22 19:38:03 -04:00
parent 6c2290fb6e
commit bd5b6d1aba
4 changed files with 0 additions and 349 deletions
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111
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java
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package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
/**
* IF THERE IS NO JAVADOC RIGHT HERE, YELL AT chartl
*
* @Author chartl
* @Date May 26, 2010
*/
@Analysis(name = "Indel length histograms", description = "Shows the distribution of insertion/deletion event lengths (negative for deletion, positive for insertion)")
public class IndelLengthHistogram extends VariantEvaluator {
private static final int SIZE_LIMIT = 100;
@DataPoint(description="Histogram of indel lengths")
IndelHistogram indelHistogram = new IndelHistogram(SIZE_LIMIT);
/*
* Indel length histogram table object
*/
static class IndelHistogram implements TableType {
private Integer[] colKeys;
private int limit;
private String[] rowKeys = {"EventLength"};
private Integer[] indelHistogram;
public IndelHistogram(int limit) {
colKeys = initColKeys(limit);
indelHistogram = initHistogram(limit);
this.limit = limit;
}
public Object[] getColumnKeys() {
return colKeys;
}
public Object[] getRowKeys() {
return rowKeys;
}
public Object getCell(int row, int col) {
return indelHistogram[col];
}
private Integer[] initColKeys(int size) {
Integer[] cK = new Integer[size*2+1];
int index = 0;
for ( int i = -size; i <= size; i ++ ) {
cK[index] = i;
index++;
}
return cK;
}
private Integer[] initHistogram(int size) {
Integer[] hist = new Integer[size*2+1];
for ( int i = 0; i < 2*size+1; i ++ ) {
hist[i] = 0;
}
return hist;
}
public String getName() { return "indelHistTable"; }
public void update(int eLength) {
indelHistogram[len2index(eLength)]++;
}
private int len2index(int len) {
if ( len > limit || len < -limit ) {
throw new ReviewedStingException("Indel length exceeds limit of "+limit+" please increase indel limit size");
}
return len + limit;
}
}
public boolean enabled() { return true; }
public String getName() { return "IndelLengthHistogram"; }
public int getComparisonOrder() { return 1; } // need only the evals
public String update1(VariantContext vc1, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( vc1.isIndel() && vc1.isPolymorphicInSamples() ) {
if ( ! vc1.isBiallelic() ) {
//veWalker.getLogger().warn("[IndelLengthHistogram] Non-biallelic indel at "+ref.getLocus()+" ignored.");
return vc1.toString(); // biallelic sites are output
}
// only count simple insertions/deletions, not complex indels
if ( vc1.isSimpleInsertion() ) {
indelHistogram.update(vc1.getAlternateAllele(0).length());
} else if ( vc1.isSimpleDeletion() ) {
indelHistogram.update(-vc1.getReference().length());
}
}
return null;
}
}

154
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicAFs.java
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/*
* Copyright (c) 2011, 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.varianteval.evaluators;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.*;
import java.util.*;
@Analysis(description = "Evaluation summary for multi-allelic variants")
public class MultiallelicAFs extends VariantEvaluator {
final protected static Logger logger = Logger.getLogger(MultiallelicAFs.class);
public enum Type {
SNP, INDEL
}
@DataPoint(description="Histogram of allele frequencies for most common SNP alternate allele")
AFHistogram AFhistogramMaxSnp = new AFHistogram();
@DataPoint(description="Histogram of allele frequencies for less common SNP alternate alleles")
AFHistogram AFhistogramMinSnp = new AFHistogram();
@DataPoint(description="Histogram of allele frequencies for most common Indel alternate allele")
AFHistogram AFhistogramMaxIndel = new AFHistogram();
@DataPoint(description="Histogram of allele frequencies for less common Indel alternate alleles")
AFHistogram AFhistogramMinIndel = new AFHistogram();
/*
* AF histogram table object
*/
static class AFHistogram implements TableType {
private Object[] rowKeys, colKeys = {"count"};
private int[] AFhistogram;
private static final double AFincrement = 0.01;
private static final int numBins = (int)(1.00 / AFincrement);
public AFHistogram() {
rowKeys = initRowKeys();
AFhistogram = new int[rowKeys.length];
}
public Object[] getColumnKeys() {
return colKeys;
}
public Object[] getRowKeys() {
return rowKeys;
}
public Object getCell(int row, int col) {
return AFhistogram[row];
}
private static Object[] initRowKeys() {
ArrayList<String> keyList = new ArrayList<String>(numBins + 1);
for ( double a = 0.00; a <= 1.01; a += AFincrement ) {
keyList.add(String.format("%.2f", a));
}
return keyList.toArray();
}
public String getName() { return "AFHistTable"; }
public void update(final double AF) {
final int bin = (int)(numBins * MathUtils.round(AF, 2));
AFhistogram[bin]++;
}
}
public void initialize(VariantEvalWalker walker) {}
@Override public boolean enabled() { return true; }
public int getComparisonOrder() {
return 2;
}
public void update0(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {}
public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( eval == null || eval.isMonomorphicInSamples() )
return null;
if ( !eval.isBiallelic() )
return null;
// update counts
switch ( eval.getType() ) {
case SNP:
updateAFhistogram(eval, AFhistogramMaxSnp, AFhistogramMinSnp);
break;
case INDEL:
updateAFhistogram(eval, AFhistogramMaxIndel, AFhistogramMinIndel);
break;
default:
throw new UserException.BadInput("Unexpected variant context type: " + eval);
}
return null; // we don't capture any interesting sites
}
private void updateAFhistogram(VariantContext vc, AFHistogram max, AFHistogram min) {
final Object obj = vc.getAttribute(VCFConstants.ALLELE_FREQUENCY_KEY, null);
if ( obj == null || !(obj instanceof List) )
return;
List<String> list = (List<String>)obj;
ArrayList<Double> AFs = new ArrayList<Double>(list.size());
for ( String str : list ) {
AFs.add(Double.valueOf(str));
}
Collections.sort(AFs);
max.update(AFs.get(AFs.size()-1));
for ( int i = 0; i < AFs.size() - 1; i++ )
min.update(AFs.get(i));
}
}

54
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PhaseStats.java
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package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
/**
* Created by IntelliJ IDEA. User: kiran Date: Nov 29, 2010 Time: 3:25:59 PM To change this template use File | Settings
* | File Templates.
*/
class NewPhaseStats {
public int neitherPhased;
public int onlyCompPhased;
public int onlyEvalPhased;
public int phasesAgree;
public int phasesDisagree;
public NewPhaseStats() {
this.neitherPhased = 0;
this.onlyCompPhased = 0;
this.onlyEvalPhased = 0;
this.phasesAgree = 0;
this.phasesDisagree = 0;
}
public String toString() {
StringBuilder sb = new StringBuilder();
sb.append("Neither phased: " + neitherPhased + "\tOnly Comp: " + onlyCompPhased + "\tOnly Eval: " + onlyEvalPhased + "\tSame phase: " + phasesAgree + "\tOpposite phase: " + phasesDisagree);
return sb.toString();
}
public static String[] getFieldNamesArray() {
return new String[]{"total", "neither", "only_comp", "only_eval", "both", "match", "switch", "switch_rate"};
}
public Object getField(int index) {
switch (index) {
case (0):
return (neitherPhased + onlyCompPhased + onlyEvalPhased + phasesAgree + phasesDisagree);
case (1):
return neitherPhased;
case (2):
return onlyCompPhased;
case (3):
return onlyEvalPhased;
case (4):
return (phasesAgree + phasesDisagree);
case (5):
return phasesAgree;
case (6):
return phasesDisagree;
case (7):
return ((phasesDisagree == 0) ? 0 : ((double) phasesDisagree) / (phasesAgree + phasesDisagree));
default:
return -1;
}
}
}

30
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SamplePreviousGenotypes.java
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package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import java.util.HashMap;
/**
* Created by IntelliJ IDEA. User: kiran Date: Nov 29, 2010 Time: 3:25:59 PM To change this template use File | Settings
* | File Templates.
*/
class NewSamplePreviousGenotypes {
private HashMap<String, CompEvalGenotypes> sampleGenotypes = null;
public NewSamplePreviousGenotypes() {
this.sampleGenotypes = new HashMap<String, CompEvalGenotypes>();
}
public CompEvalGenotypes get(String sample) {
return sampleGenotypes.get(sample);
}
public void put(String sample, CompEvalGenotypes compEvalGts) {
sampleGenotypes.put(sample, compEvalGts);
}
public void put(String sample, GenomeLoc locus, Genotype compGt, Genotype evalGt) {
sampleGenotypes.put(sample, new CompEvalGenotypes(locus, compGt, evalGt));
}
}