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More eval modules being removed from VariantEval 

-- IndelStatistics is superceded by IndelStatistics
This commit is contained in:
Mark DePristo 2012-03-22 19:40:19 -04:00
parent bd5b6d1aba
commit 9ddd5aec93
1 changed files with 0 additions and 295 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.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.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.IndelUtils;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.ArrayList;
/*
* 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.
*/
@Analysis(name = "IndelStatistics", description = "Shows various indel metrics and statistics")
public class IndelStatistics extends VariantEvaluator {
@DataPoint(description = "Indel Statistics")
IndelStats indelStats = null;
// @DataPoint(description = "Indel Classification")
IndelClasses indelClasses = null;
int numSamples = 0;
public void initialize(VariantEvalWalker walker) {
numSamples = walker.getNumSamples();
}
private static final int INDEL_SIZE_LIMIT = 100;
private static final int IND_HET = 0;
private static final int IND_INS = 1;
private static final int IND_DEL = 2;
private static final int IND_COMPLEX = 3;
private static final int IND_HET_INS = 4;
private static final int IND_HOM_INS = 5;
private static final int IND_HET_DEL = 6;
private static final int IND_HOM_DEL = 7;
private static final int IND_HOM_REF = 8;
private static final int IND_MIXED = 9;
private static final int IND_LONG = 10;
private static final int IND_AT_EXP = 11;
private static final int IND_CG_EXP = 12;
private static final int IND_FRAMESHIFT = 13;
private static final int NUM_SCALAR_COLUMNS = 14;
static int len2Index(int ind) {
return ind+INDEL_SIZE_LIMIT+NUM_SCALAR_COLUMNS;
}
static int index2len(int ind) {
return ind-INDEL_SIZE_LIMIT-NUM_SCALAR_COLUMNS;
}
static class IndelStats implements TableType {
protected final static String[] COLUMN_KEYS;
static {
COLUMN_KEYS= new String[NUM_SCALAR_COLUMNS+2*INDEL_SIZE_LIMIT+1];
COLUMN_KEYS[0] = "heterozygosity";
COLUMN_KEYS[1] = "insertions";
COLUMN_KEYS[2] = "deletions";
COLUMN_KEYS[3] = "complex";
COLUMN_KEYS[4] = "het_insertions";
COLUMN_KEYS[5] = "homozygous_insertions";
COLUMN_KEYS[6] = "het_deletions";
COLUMN_KEYS[7] = "homozygous_deletions";
COLUMN_KEYS[8] = "homozygous_reference_sites";
COLUMN_KEYS[9] = "complex_events";
COLUMN_KEYS[10] = "long_indels";
COLUMN_KEYS[11] = "AT_expansions";
COLUMN_KEYS[12] = "CG_expansions";
COLUMN_KEYS[13] = "frameshift_indels";
for (int k=NUM_SCALAR_COLUMNS; k < NUM_SCALAR_COLUMNS+ 2*INDEL_SIZE_LIMIT+1; k++)
COLUMN_KEYS[k] = "indel_size_len"+Integer.valueOf(index2len(k));
}
// map of sample to statistics
protected final int[] indelSummary;
public IndelStats(final VariantContext vc) {
indelSummary = new int[COLUMN_KEYS.length];
}
/**
*
* @return one row per sample
*/
public Object[] getRowKeys() {
return new String[]{"all"};
}
public Object getCell(int x, int y) {
return String.format("%d",indelSummary[y]);
}
/**
* get the column keys
* @return a list of objects, in this case strings, that are the column names
*/
public Object[] getColumnKeys() {
return COLUMN_KEYS;
}
public String getName() {
return "IndelStats";
}
public int getComparisonOrder() {
return 1; // we only need to see each eval track
}
public String toString() {
return getName();
}
/*
* increment the specified value
*/
public void incrValue(VariantContext vc, ReferenceContext ref) {
int eventLength = 0;
boolean isInsertion = false, isDeletion = false;
if ( vc.isSimpleInsertion() ) {
eventLength = vc.getAlternateAllele(0).length();
indelSummary[IND_INS]++;
isInsertion = true;
} else if ( vc.isSimpleDeletion() ) {
indelSummary[IND_DEL]++;
eventLength = -vc.getReference().length();
isDeletion = true;
}
else if (vc.isComplexIndel()) {
indelSummary[IND_COMPLEX]++;
}
else if (vc.isMixed())
indelSummary[IND_MIXED]++;
if (IndelUtils.isATExpansion(vc,ref))
indelSummary[IND_AT_EXP]++;
if (IndelUtils.isCGExpansion(vc,ref))
indelSummary[IND_CG_EXP]++;
// make sure event doesn't overstep array boundaries
if (vc.isSimpleDeletion() || vc.isSimpleInsertion()) {
if (Math.abs(eventLength) < INDEL_SIZE_LIMIT) {
indelSummary[len2Index(eventLength)]++;
if (eventLength % 3 != 0)
indelSummary[IND_FRAMESHIFT]++;
}
else
indelSummary[IND_LONG]++;
}
}
}
static class IndelClasses implements TableType {
protected final static String[] columnNames = IndelUtils.getIndelClassificationNames();
// map of sample to statistics
protected final int[] indelClassSummary;
public IndelClasses(final VariantContext vc) {
indelClassSummary = new int[columnNames.length];
}
/**
*
* @return one row per sample
*/
public Object[] getRowKeys() {
return new String[]{"all"};
}
public Object getCell(int x, int y) {
return String.format("%d",indelClassSummary[y]);
}
/**
* get the column keys
* @return a list of objects, in this case strings, that are the column names
*/
public Object[] getColumnKeys() {
return columnNames;
}
public String getName() {
return "IndelClasses";
}
public int getComparisonOrder() {
return 1; // we only need to see each eval track
}
public String toString() {
return getName();
}
private void incrementSampleStat(VariantContext vc, int index) {
indelClassSummary[index]++;
}
/*
* increment the specified value
*/
public void incrValue(VariantContext vc, ReferenceContext ref) {
ArrayList<Integer> indices = IndelUtils.findEventClassificationIndex(vc,ref);
//System.out.format("pos:%d \nREF: %s, ALT: %s\n",vc.getStart(), vc.getReference().getDisplayString(),
// vc.getAlternateAllele(0).getDisplayString());
byte[] refBases = ref.getBases();
//System.out.format("ref bef:%s\n",new String(Arrays.copyOfRange(refBases,0,refBases.length/2+1) ));
//System.out.format("ref aft:%s\n",new String(Arrays.copyOfRange(refBases,refBases.length/2+1,refBases.length) ));
for (int index: indices) {
incrementSampleStat(vc, index);
// System.out.println(IndelUtils.getIndelClassificationName(index));
}
}
}
//public IndelStatistics(VariantEvalWalker parent) {
//super(parent);
// don't do anything
//}
public String getName() {
return "IndelStatistics";
}
public int getComparisonOrder() {
return 1; // we only need to see each eval track
}
public boolean enabled() {
return true;
}
public String toString() {
return getName();
}
public String update1(VariantContext eval, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if (eval != null && eval.isPolymorphicInSamples()) {
if ( indelStats == null ) {
indelStats = new IndelStats(eval);
}
if ( indelClasses == null ) {
indelClasses = new IndelClasses(eval);
}
if ( eval.isIndel() || eval.isMixed() ) {
if (indelStats != null )
indelStats.incrValue(eval, ref);
if (indelClasses != null)
indelClasses.incrValue(eval, ref);
}
}
return null; // This module doesn't capture any interesting sites, so return null
}
public void finalizeEvaluation() {
int k=0;
}
}