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-- No more IndelLengthHistogram (superceded by IndelSummary in subsequent commit) -- No more SamplePreviousGenotypes or PhaseStats -- No more MultiallelicAFs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
parent
6c2290fb6e
commit
bd5b6d1aba
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package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
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import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
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import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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/**
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* IF THERE IS NO JAVADOC RIGHT HERE, YELL AT chartl
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*
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* @Author chartl
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* @Date May 26, 2010
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*/
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@Analysis(name = "Indel length histograms", description = "Shows the distribution of insertion/deletion event lengths (negative for deletion, positive for insertion)")
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public class IndelLengthHistogram extends VariantEvaluator {
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private static final int SIZE_LIMIT = 100;
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@DataPoint(description="Histogram of indel lengths")
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IndelHistogram indelHistogram = new IndelHistogram(SIZE_LIMIT);
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/*
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* Indel length histogram table object
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*/
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static class IndelHistogram implements TableType {
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private Integer[] colKeys;
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private int limit;
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private String[] rowKeys = {"EventLength"};
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private Integer[] indelHistogram;
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public IndelHistogram(int limit) {
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colKeys = initColKeys(limit);
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indelHistogram = initHistogram(limit);
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this.limit = limit;
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}
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public Object[] getColumnKeys() {
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return colKeys;
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}
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public Object[] getRowKeys() {
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return rowKeys;
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}
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public Object getCell(int row, int col) {
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return indelHistogram[col];
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}
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private Integer[] initColKeys(int size) {
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Integer[] cK = new Integer[size*2+1];
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int index = 0;
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for ( int i = -size; i <= size; i ++ ) {
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cK[index] = i;
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index++;
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}
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return cK;
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}
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private Integer[] initHistogram(int size) {
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Integer[] hist = new Integer[size*2+1];
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for ( int i = 0; i < 2*size+1; i ++ ) {
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hist[i] = 0;
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}
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return hist;
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}
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public String getName() { return "indelHistTable"; }
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public void update(int eLength) {
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indelHistogram[len2index(eLength)]++;
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}
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private int len2index(int len) {
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if ( len > limit || len < -limit ) {
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throw new ReviewedStingException("Indel length exceeds limit of "+limit+" please increase indel limit size");
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}
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return len + limit;
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}
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}
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public boolean enabled() { return true; }
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public String getName() { return "IndelLengthHistogram"; }
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public int getComparisonOrder() { return 1; } // need only the evals
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public String update1(VariantContext vc1, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if ( vc1.isIndel() && vc1.isPolymorphicInSamples() ) {
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if ( ! vc1.isBiallelic() ) {
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//veWalker.getLogger().warn("[IndelLengthHistogram] Non-biallelic indel at "+ref.getLocus()+" ignored.");
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return vc1.toString(); // biallelic sites are output
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}
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// only count simple insertions/deletions, not complex indels
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if ( vc1.isSimpleInsertion() ) {
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indelHistogram.update(vc1.getAlternateAllele(0).length());
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} else if ( vc1.isSimpleDeletion() ) {
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indelHistogram.update(-vc1.getReference().length());
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}
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}
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return null;
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}
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}
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@ -1,154 +0,0 @@
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/*
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* Copyright (c) 2011, The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
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import org.apache.log4j.Logger;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
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import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
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import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
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import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
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import org.broadinstitute.sting.utils.MathUtils;
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import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.variantcontext.*;
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import java.util.*;
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@Analysis(description = "Evaluation summary for multi-allelic variants")
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public class MultiallelicAFs extends VariantEvaluator {
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final protected static Logger logger = Logger.getLogger(MultiallelicAFs.class);
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public enum Type {
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SNP, INDEL
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}
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@DataPoint(description="Histogram of allele frequencies for most common SNP alternate allele")
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AFHistogram AFhistogramMaxSnp = new AFHistogram();
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@DataPoint(description="Histogram of allele frequencies for less common SNP alternate alleles")
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AFHistogram AFhistogramMinSnp = new AFHistogram();
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@DataPoint(description="Histogram of allele frequencies for most common Indel alternate allele")
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AFHistogram AFhistogramMaxIndel = new AFHistogram();
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@DataPoint(description="Histogram of allele frequencies for less common Indel alternate alleles")
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AFHistogram AFhistogramMinIndel = new AFHistogram();
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/*
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* AF histogram table object
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*/
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static class AFHistogram implements TableType {
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private Object[] rowKeys, colKeys = {"count"};
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private int[] AFhistogram;
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private static final double AFincrement = 0.01;
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private static final int numBins = (int)(1.00 / AFincrement);
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public AFHistogram() {
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rowKeys = initRowKeys();
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AFhistogram = new int[rowKeys.length];
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}
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public Object[] getColumnKeys() {
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return colKeys;
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}
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public Object[] getRowKeys() {
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return rowKeys;
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}
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public Object getCell(int row, int col) {
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return AFhistogram[row];
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}
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private static Object[] initRowKeys() {
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ArrayList<String> keyList = new ArrayList<String>(numBins + 1);
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for ( double a = 0.00; a <= 1.01; a += AFincrement ) {
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keyList.add(String.format("%.2f", a));
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}
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return keyList.toArray();
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}
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public String getName() { return "AFHistTable"; }
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public void update(final double AF) {
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final int bin = (int)(numBins * MathUtils.round(AF, 2));
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AFhistogram[bin]++;
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}
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}
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public void initialize(VariantEvalWalker walker) {}
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@Override public boolean enabled() { return true; }
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public int getComparisonOrder() {
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return 2;
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}
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public void update0(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {}
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public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if ( eval == null || eval.isMonomorphicInSamples() )
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return null;
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if ( !eval.isBiallelic() )
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return null;
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// update counts
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switch ( eval.getType() ) {
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case SNP:
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updateAFhistogram(eval, AFhistogramMaxSnp, AFhistogramMinSnp);
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break;
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case INDEL:
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updateAFhistogram(eval, AFhistogramMaxIndel, AFhistogramMinIndel);
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break;
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default:
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throw new UserException.BadInput("Unexpected variant context type: " + eval);
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}
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return null; // we don't capture any interesting sites
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}
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private void updateAFhistogram(VariantContext vc, AFHistogram max, AFHistogram min) {
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final Object obj = vc.getAttribute(VCFConstants.ALLELE_FREQUENCY_KEY, null);
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if ( obj == null || !(obj instanceof List) )
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return;
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List<String> list = (List<String>)obj;
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ArrayList<Double> AFs = new ArrayList<Double>(list.size());
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for ( String str : list ) {
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AFs.add(Double.valueOf(str));
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}
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Collections.sort(AFs);
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max.update(AFs.get(AFs.size()-1));
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for ( int i = 0; i < AFs.size() - 1; i++ )
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min.update(AFs.get(i));
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}
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}
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package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
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/**
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* Created by IntelliJ IDEA. User: kiran Date: Nov 29, 2010 Time: 3:25:59 PM To change this template use File | Settings
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* | File Templates.
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*/
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class NewPhaseStats {
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public int neitherPhased;
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public int onlyCompPhased;
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public int onlyEvalPhased;
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public int phasesAgree;
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public int phasesDisagree;
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public NewPhaseStats() {
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this.neitherPhased = 0;
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this.onlyCompPhased = 0;
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this.onlyEvalPhased = 0;
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this.phasesAgree = 0;
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this.phasesDisagree = 0;
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}
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public String toString() {
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StringBuilder sb = new StringBuilder();
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sb.append("Neither phased: " + neitherPhased + "\tOnly Comp: " + onlyCompPhased + "\tOnly Eval: " + onlyEvalPhased + "\tSame phase: " + phasesAgree + "\tOpposite phase: " + phasesDisagree);
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return sb.toString();
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}
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public static String[] getFieldNamesArray() {
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return new String[]{"total", "neither", "only_comp", "only_eval", "both", "match", "switch", "switch_rate"};
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}
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public Object getField(int index) {
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switch (index) {
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case (0):
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return (neitherPhased + onlyCompPhased + onlyEvalPhased + phasesAgree + phasesDisagree);
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case (1):
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return neitherPhased;
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case (2):
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return onlyCompPhased;
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case (3):
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return onlyEvalPhased;
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case (4):
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return (phasesAgree + phasesDisagree);
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case (5):
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return phasesAgree;
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case (6):
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return phasesDisagree;
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case (7):
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return ((phasesDisagree == 0) ? 0 : ((double) phasesDisagree) / (phasesAgree + phasesDisagree));
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default:
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return -1;
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}
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}
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}
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package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.variantcontext.Genotype;
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import java.util.HashMap;
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/**
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* Created by IntelliJ IDEA. User: kiran Date: Nov 29, 2010 Time: 3:25:59 PM To change this template use File | Settings
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* | File Templates.
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*/
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class NewSamplePreviousGenotypes {
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private HashMap<String, CompEvalGenotypes> sampleGenotypes = null;
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public NewSamplePreviousGenotypes() {
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this.sampleGenotypes = new HashMap<String, CompEvalGenotypes>();
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}
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public CompEvalGenotypes get(String sample) {
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return sampleGenotypes.get(sample);
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}
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public void put(String sample, CompEvalGenotypes compEvalGts) {
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sampleGenotypes.put(sample, compEvalGts);
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}
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public void put(String sample, GenomeLoc locus, Genotype compGt, Genotype evalGt) {
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sampleGenotypes.put(sample, new CompEvalGenotypes(locus, compGt, evalGt));
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}
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}
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