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Added in an eval module that calculates the dispersion histograms between eval and comp (e.g. M_{i,j} = # of times eval observed to have AC i, comp AC j -- for af it's i/100 vs j/100 ) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4507 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-10-15 19:07:43 +00:00
parent f78ff08e2b
commit 8b2d387643
2 changed files with 139 additions and 5 deletions
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10
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java
View File

@ -404,15 +404,15 @@ public class GenotypeConcordance extends VariantEvaluator implements StandardEva
}
private int getAC(VariantContext vc) {
if ( vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY).getClass().isAssignableFrom(List.class) ) {
if ( List.class.isAssignableFrom(vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY).getClass()) ) {
return ((List<Integer>) vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY)).get(0);
} else if ( vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY).getClass().isAssignableFrom(Integer.class)) {
} else if ( Integer.class.isAssignableFrom(vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY).getClass())) {
return (Integer) vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY);
} else if ( vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY).getClass().isAssignableFrom(String.class)) {
} else if ( String.class.isAssignableFrom(vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY).getClass()) ) {
// two ways of parsing
String ac = (String) vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY);
if ( ac.startsWith("[") ) {
return Integer.parseInt(ac.replaceAll("[","").replaceAll("]",""));
return Integer.parseInt(ac.replaceAll("\\[","").replaceAll("\\]",""));
} else {
try {
return Integer.parseInt(ac);
@ -421,7 +421,7 @@ public class GenotypeConcordance extends VariantEvaluator implements StandardEva
}
}
} else {
throw new UserException(String.format("The format of the AC field does not appear to be of integer-list or String format"));
throw new UserException(String.format("The format of the AC field does not appear to be of integer-list or String format, class was %s",vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY).getClass()));
}
}
}

134
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/AlleleFrequencyComparison.java 100755
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@ -0,0 +1,134 @@
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.VCFConstants;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.report.tags.Analysis;
import org.broadinstitute.sting.utils.report.tags.DataPoint;
import org.broadinstitute.sting.utils.report.utils.TableType;
import java.util.List;
/**
*
*/
@Analysis(name = "Allele Frequency Comparison", description = "Compare allele frequency and counts between eval and comp")
public class AlleleFrequencyComparison extends VariantEvaluator {
private static int MAX_AC_COUNT = 100; // todo -- command line argument?
@DataPoint(description="Counts of eval frequency versus comp frequency")
AFTable afTable = new AFTable();
@DataPoint(description="Counts of eval AC versus comp AC")
ACTable acTable = new ACTable(MAX_AC_COUNT);
public boolean enabled() { return true; }
public int getComparisonOrder() { return 2; }
public String getName() { return "Allele Frequency Comparison"; }
public AlleleFrequencyComparison(VariantEvalWalker parent) {
super(parent);
}
public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, VariantEvalWalker.EvaluationContext group) {
if ( ! (isValidVC(eval) && isValidVC(comp)) ) {
return null;
} else {
afTable.update(getAF(eval),getAF(comp));
acTable.update(getAC(eval),getAC(comp));
}
return null; // there is nothing interesting
}
private static boolean isValidVC(final VariantContext vc) {
return (vc != null && !vc.isFiltered() && vc.getAlternateAlleles().size() == 1 && vc.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) && vc.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY));
}
private static double getAF(VariantContext vc) {
return ((List<Double>) vc.getAttribute(VCFConstants.ALLELE_FREQUENCY_KEY)).get(0);
}
private static int getAC(VariantContext vc) {
return ((List<Integer>) vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY)).get(0);
}
}
class AFTable implements TableType {
protected int[][] afCounts = new int[101][101];
public Object[] getRowKeys() {
String[] afKeys = new String[101];
for ( int f = 0; f < 101; f ++ ) {
afKeys[f] = String.format("%.2f",(f+0.0)/100.0);
}
return afKeys;
}
public Object[] getColumnKeys() {
return getRowKeys(); // nice thing about symmetric tables
}
public Object getCell(int i, int j) {
return afCounts[i][j];
}
public String getName() {
return "Allele Frequency Concordance";
}
public void update(double eval, double comp) {
afCounts[af2index(eval)][af2index(comp)]++;
}
private int af2index(double d) {
return (int) Math.round(100*d);
}
}
class ACTable implements TableType {
protected int[][] acCounts;
protected int maxAC;
public ACTable(int acMaximum) {
maxAC = acMaximum;
acCounts = new int[acMaximum+1][acMaximum+1];
}
public Object[] getRowKeys() {
String[] acKeys = new String[maxAC+1];
for ( int i = 0 ; i <= maxAC ; i ++ ) {
acKeys[i] = String.format("%d",i);
}
return acKeys;
}
public Object[] getColumnKeys() {
return getRowKeys();
}
public Object getCell(int i, int j) {
return acCounts[i][j];
}
public String getName() {
return "Allele Counts Concordance";
}
public void update(int eval, int comp) {
eval = eval > maxAC ? maxAC : eval;
comp = comp > maxAC ? maxAC : comp;
acCounts[eval][comp]++;
}
}