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Knocking out some quick findBugs. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3887 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-07-27 14:10:59 +00:00
parent 894623858d
commit f5566a6593
7 changed files with 11 additions and 335 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TileCovariate.java
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@ -34,7 +34,7 @@ import net.sf.picard.util.IlluminaUtil;
public class TileCovariate implements ExperimentalCovariate { public class TileCovariate implements ExperimentalCovariate {
private static boolean exceptionWhenNoTile = false; private boolean exceptionWhenNoTile = false;
// Initialize any member variables using the command-line arguments passed to the walkers // Initialize any member variables using the command-line arguments passed to the walkers
public void initialize( final RecalibrationArgumentCollection RAC ) { public void initialize( final RecalibrationArgumentCollection RAC ) {

13
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantQualityScore.java
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@ -53,8 +53,8 @@ public class VariantQualityScore extends VariantEvaluator {
@DataPoint(name="Quality by Allele Count", description = "average variant quality for each allele count") @DataPoint(name="Quality by Allele Count", description = "average variant quality for each allele count")
AlleleCountStats alleleCountStats = null; AlleleCountStats alleleCountStats = null;
class TiTvStats implements TableType { static class TiTvStats implements TableType {
final int NUM_BINS = 20; final static int NUM_BINS = 20;
final HashMap<Integer, Pair<Long,Long>> qualByIsTransition = new HashMap<Integer, Pair<Long,Long>>(); // A hashMap holds all the qualities until we are able to bin them appropriately final HashMap<Integer, Pair<Long,Long>> qualByIsTransition = new HashMap<Integer, Pair<Long,Long>>(); // A hashMap holds all the qualities until we are able to bin them appropriately
final long transitionByQuality[] = new long[NUM_BINS]; final long transitionByQuality[] = new long[NUM_BINS];
final long transversionByQuality[] = new long[NUM_BINS]; final long transversionByQuality[] = new long[NUM_BINS];
@ -81,13 +81,14 @@ public class VariantQualityScore extends VariantEvaluator {
} }
public String toString() { public String toString() {
String returnString = ""; StringBuffer returnString = new StringBuffer();
// output the ti/tv array // output the ti/tv array
returnString += "titvByQuality: "; returnString.append("titvByQuality: ");
for( int iii = 0; iii < NUM_BINS; iii++ ) { for( int iii = 0; iii < NUM_BINS; iii++ ) {
returnString += titvByQuality[iii] + " "; returnString.append(titvByQuality[iii]);
returnString.append(" ");
} }
return returnString; return returnString.toString();
} }
public void incrValue( final double qual, final boolean isTransition ) { public void incrValue( final double qual, final boolean isTransition ) {

1
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModel.java
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@ -586,6 +586,7 @@ public final class VariantGaussianMixtureModel extends VariantOptimizationModel
} }
annIndex++; annIndex++;
outputFile.close();
} }
// BUGBUG: next output the actual cluster on top by integrating out every other annotation // BUGBUG: next output the actual cluster on top by integrating out every other annotation

78
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantNearestNeighborsModel.java
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@ -1,78 +0,0 @@
package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
import org.broadinstitute.sting.utils.StingException;
import java.io.PrintStream;
/*
* 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.
*/
/**
* Created by IntelliJ IDEA.
* User: rpoplin
* Date: Mar 1, 2010
*/
public final class VariantNearestNeighborsModel extends VariantOptimizationModel {
private final int numKNN;
public VariantNearestNeighborsModel( VariantDataManager _dataManager, final double _targetTITV, final int _numKNN ) {
super( _targetTITV );
//dataManager = _dataManager;
numKNN = _numKNN;
}
public void run( final String outputPrefix ) {
throw new StingException( "Nearest Neighbors model hasn't been updated yet." );
/*
final int numVariants = dataManager.numVariants;
final double[] pTrueVariant = new double[numVariants];
final VariantTree vTree = new VariantTree( numKNN );
vTree.createTreeFromData( dataManager.data );
System.out.println("Finished creating the kd-tree.");
for(int iii = 0; iii < numVariants; iii++) {
pTrueVariant[iii] = calcTruePositiveRateFromTITV( vTree.calcNeighborhoodTITV( dataManager.data[iii] ) );
}
PrintStream outputFile;
try {
outputFile = new PrintStream( outputPrefix + ".knn.optimize" );
} catch (Exception e) {
throw new StingException( "Unable to create output file: " + outputPrefix + ".knn.optimize" );
}
for(int iii = 0; iii < numVariants; iii++) {
outputFile.print(String.format("%.4f",pTrueVariant[iii]) + ",");
outputFile.println( (dataManager.data[iii].isTransition ? 1 : 0)
+ "," + (dataManager.data[iii].isKnown? 1 : 0));
}
*/
}
}

144
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantTree.java
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@ -1,144 +0,0 @@
package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
import org.broadinstitute.sting.utils.StingException;
/*
* 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.
*/
/**
* Created by IntelliJ IDEA.
* User: rpoplin
* Date: Feb 24, 2010
*/
public class VariantTree {
private final VariantTreeNode root;
private final int numKNN;
public VariantTree( final int _numKNN ) {
root = new VariantTreeNode();
numKNN = _numKNN;
}
public void createTreeFromData( VariantDatum[] data ) {
root.cutData( data, 0, 0, data[0].annotations.length );
}
public double calcNeighborhoodTITV( final VariantDatum variant ) {
double[] distances;
// Grab the subset of points that are approximately near this point
final VariantDatum[] data = getBin( variant.annotations, root );
if( data.length < numKNN ) {
throw new StingException( "Bin is too small. Should be > " + numKNN );
}
// Find the X nearest points in the subset
final double[] originalDistances = calcDistances( variant.annotations, data );
distances = originalDistances.clone();
quickSort( distances, 0, distances.length-1 ); // BUGBUG: distances.length or distances.length-1
final double minDistance = distances[numKNN - 1];
// Calculate probability of being true based on this set of SNPs
int numTi = 0;
int numTv = 0;
for( int iii = 0; iii < distances.length; iii++ ) {
if( originalDistances[iii] <= minDistance ) {
if( data[iii].isTransition ) { numTi++; }
else { numTv++; }
}
}
return ((double) numTi) / ((double) numTv);
}
private VariantDatum[] getBin( final double[] variant, final VariantTreeNode node ) {
if( node.variants != null ) {
return node.variants;
} else {
if( variant[node.cutDim] < node.cutValue ) {
return getBin( variant, node.left );
} else {
return getBin( variant, node.right );
}
}
}
private double[] calcDistances( final double[] variant, final VariantDatum[] data ) {
final double[] distSquared = new double[data.length];
int iii = 0;
for( final VariantDatum variantDatum : data ) {
distSquared[iii] = 0.0;
int jjj = 0;
for( final double value : variantDatum.annotations) {
final double diff = variant[jjj] - value;
distSquared[iii] += ( diff * diff );
jjj++;
}
iii++;
}
return distSquared;
}
public static int partition(final double arr[], final int left, final int right)
{
int i = left, j = right;
double tmp;
final double pivot = arr[(left + right) / 2];
while (i <= j) {
while (arr[i] < pivot) {
i++;
}
while (arr[j] > pivot) {
j--;
}
if (i <= j) {
tmp = arr[i];
arr[i] = arr[j];
arr[j] = tmp;
i++;
j--;
}
}
return i;
}
public static void quickSort(final double arr[], final int left, final int right) {
final int index = partition(arr, left, right);
if (left < index - 1) {
quickSort(arr, left, index - 1);
}
if (index < right) {
quickSort(arr, index, right);
}
}
}

104
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantTreeNode.java
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@ -1,104 +0,0 @@
package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
/*
* 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.
*/
/**
* Created by IntelliJ IDEA.
* User: rpoplin
* Date: Feb 24, 2010
*/
public class VariantTreeNode {
public VariantTreeNode left;
public VariantTreeNode right;
public int cutDim;
public double cutValue;
public VariantDatum[] variants;
private final int minBinSize = 8000; // BUGBUG: must be larger than number of kNN
public VariantTreeNode() {
left = null;
right = null;
variants = null;
cutDim = -1;
cutValue = -1;
}
public final void cutData( final VariantDatum[] data, final int depth, final int lastCutDepth, final int numAnnotations ) {
cutDim = depth % numAnnotations;
if( depth != lastCutDepth && (cutDim == (lastCutDepth % numAnnotations)) ) { // Base case: we've tried to cut on all the annotations
variants = data;
return;
}
final double[] values = new double[data.length];
for( int iii = 0; iii < data.length; iii++ ) {
values[iii] = data[iii].annotations[cutDim];
}
final double[] sortedValues = values.clone();
VariantTree.quickSort( sortedValues, 0, values.length-1 ); // BUGBUG: values.length or values.length-1
final int lowPivotIndex = Math.round(0.40f * sortedValues.length);
final int highPivotIndex = Math.round(0.60f * sortedValues.length);
final double lowPivot = sortedValues[lowPivotIndex];
final double highPivot = sortedValues[highPivotIndex];
cutValue = highPivot;
int numLow = 0;
int numHigh = 0;
for( int iii = 0; iii < data.length; iii++ ) {
if( values[iii] < highPivot ) { numLow++; }
if( values[iii] >= lowPivot ) { numHigh++; }
}
// If cutting here makes the bin too small then don't cut
if( numLow < minBinSize || numHigh < minBinSize || (numLow == numHigh && numLow == data.length) ) {
cutValue = sortedValues[0];
right = new VariantTreeNode();
right.cutData(data, depth+1, lastCutDepth, numAnnotations);
} else {
final VariantDatum[] leftData = new VariantDatum[numLow];
final VariantDatum[] rightData = new VariantDatum[numHigh];
int leftIndex = 0;
int rightIndex = 0;
for( int iii = 0; iii < data.length; iii++ ) {
if( values[iii] < highPivot ) { leftData[leftIndex++] = data[iii]; }
if( values[iii] >= lowPivot ) { rightData[rightIndex++] = data[iii]; }
}
left = new VariantTreeNode();
right = new VariantTreeNode();
left.cutData(leftData, depth+1, depth, numAnnotations);
right.cutData(rightData, depth+1, depth, numAnnotations);
}
}
}

4
java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReadQualityScoreWalker.java
View File

@ -68,8 +68,8 @@ public class ReadQualityScoreWalker extends ReadWalker<SAMRecord, SAMFileWriter>
@Argument(fullName = "threshold", shortName = "th", doc="Flag reads whose read quality score is below this threshold", required = false) @Argument(fullName = "threshold", shortName = "th", doc="Flag reads whose read quality score is below this threshold", required = false)
protected int qualityThreshold = 13; protected int qualityThreshold = 13;
protected static BufferedReader inputReader = null; private BufferedReader inputReader = null;
protected static String line = null; private static String line = null;
public SAMRecord map( ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker ) { public SAMRecord map( ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker ) {
return read; // all the work is done in the reduce step for this walker return read; // all the work is done in the reduce step for this walker