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Cleaning up unused code in MV

This commit is contained in:
Mark DePristo 2011-09-29 12:20:07 -04:00
parent 5043d76c3d
commit 9536845e35
1 changed files with 1 additions and 49 deletions
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50
public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java
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@ -16,9 +16,6 @@ import java.util.regex.Pattern;
* Time: 12:38 PM
*/
public class MendelianViolation {
String sampleMom;
String sampleDad;
String sampleChild;
@ -31,22 +28,15 @@ public class MendelianViolation {
private static Pattern FAMILY_PATTERN = Pattern.compile("(.*)\\+(.*)=(.*)");
static final int[] mvOffsets = new int[] { 1,2,5,6,8,11,15,18,20,21,24,25 };
static final int[] nonMVOffsets = new int[]{ 0,3,4,7,9,10,12,13,14,16,17,19,22,23,26 };
public String getSampleMom() {
return sampleMom;
}
public String getSampleDad() {
return sampleDad;
}
public String getSampleChild() {
return sampleChild;
}
public double getMinGenotypeQuality() {
return minGenotypeQuality;
}
@ -130,7 +120,7 @@ public class MendelianViolation {
* @return False if we can't determine (lack of information), or it's not a violation. True if it is a violation.
*
*/
public boolean isViolation (VariantContext vc)
public boolean isViolation(VariantContext vc)
{
return setAlleles(vc) && isViolation();
}
@ -144,42 +134,4 @@ public class MendelianViolation {
return false;
return true;
}
/**
* @return the likelihood ratio for a mendelian violation
*/
public double violationLikelihoodRatio(VariantContext vc) {
double[] logLikAssignments = new double[27];
// the matrix to set up is
// MOM DAD CHILD
// |- AA
// AA AA | AB
// |- BB
// |- AA
// AA AB | AB
// |- BB
// etc. The leaves are counted as 0-11 for MVs and 0-14 for non-MVs
double[] momGL = vc.getGenotype(sampleMom).getLikelihoods().getAsVector();
double[] dadGL = vc.getGenotype(sampleDad).getLikelihoods().getAsVector();
double[] childGL = vc.getGenotype(sampleChild).getLikelihoods().getAsVector();
int offset = 0;
for ( int oMom = 0; oMom < 3; oMom++ ) {
for ( int oDad = 0; oDad < 3; oDad++ ) {
for ( int oChild = 0; oChild < 3; oChild ++ ) {
logLikAssignments[offset++] = momGL[oMom] + dadGL[oDad] + childGL[oChild];
}
}
}
double[] mvLiks = new double[12];
double[] nonMVLiks = new double[15];
for ( int i = 0; i < 12; i ++ ) {
mvLiks[i] = logLikAssignments[mvOffsets[i]];
}
for ( int i = 0; i < 15; i++) {
nonMVLiks[i] = logLikAssignments[nonMVOffsets[i]];
}
return MathUtils.log10sumLog10(mvLiks) - MathUtils.log10sumLog10(nonMVLiks);
}
}