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Catch poorly formatted PL/GL fields

This commit is contained in:
Eric Banks 2012-04-23 09:33:50 -04:00
parent 1f23d99dfa
commit 4edb005411
2 changed files with 12 additions and 3 deletions
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6
public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
View File

@ -203,7 +203,11 @@ public class UserException extends ReviewedStingException {
public static class MalformedVCF extends UserException { public static class MalformedVCF extends UserException {
public MalformedVCF(String message, String line) { public MalformedVCF(String message, String line) {
super(String.format("The provided VCF file is malformed at approximately line %s: %s", line, message)); super(String.format("The provided VCF file is malformed at line %s: %s", line, message));
}
public MalformedVCF(String message) {
super(String.format("The provided VCF file is malformed: %s", message));
} }
public MalformedVCF(String message, int lineNo) { public MalformedVCF(String message, int lineNo) {

9
public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
View File

@ -28,6 +28,7 @@ import org.broad.tribble.TribbleException;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.util.EnumMap; import java.util.EnumMap;
@ -149,8 +150,12 @@ public class GenotypeLikelihoods {
if ( !likelihoodsAsString_PLs.equals(VCFConstants.MISSING_VALUE_v4) ) { if ( !likelihoodsAsString_PLs.equals(VCFConstants.MISSING_VALUE_v4) ) {
String[] strings = likelihoodsAsString_PLs.split(","); String[] strings = likelihoodsAsString_PLs.split(",");
double[] likelihoodsAsVector = new double[strings.length]; double[] likelihoodsAsVector = new double[strings.length];
for ( int i = 0; i < strings.length; i++ ) { try {
likelihoodsAsVector[i] = Integer.parseInt(strings[i]) / -10.0; for ( int i = 0; i < strings.length; i++ ) {
likelihoodsAsVector[i] = Integer.parseInt(strings[i]) / -10.0;
}
} catch (NumberFormatException e) {
throw new UserException.MalformedVCF("The GL/PL tag contains non-integer values");
} }
return likelihoodsAsVector; return likelihoodsAsVector;
} else } else