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ReviewedStingException -> IllegalStateException

This commit is contained in:
Mauricio Carneiro 2013-03-30 20:11:55 -04:00
parent 68bf470524
commit 52e67a6973
1 changed files with 3 additions and 4 deletions
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7
public/java/src/org/broadinstitute/sting/utils/pairhmm/PairHMM.java
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@ -28,7 +28,6 @@ package org.broadinstitute.sting.utils.pairhmm;
import com.google.java.contract.Requires;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.Arrays;
@ -129,7 +128,7 @@ public abstract class PairHMM {
if ( MathUtils.goodLog10Probability(result) )
return result;
else
throw new ReviewedStingException("PairHMM Log Probability cannot be greater than 0: " + String.format("haplotype: %s, read: %s, result: %f", Arrays.toString(haplotypeBases), Arrays.toString(readBases), result));
throw new IllegalStateException("PairHMM Log Probability cannot be greater than 0: " + String.format("haplotype: %s, read: %s, result: %f", Arrays.toString(haplotypeBases), Arrays.toString(readBases), result));
}
/**
@ -185,8 +184,8 @@ public abstract class PairHMM {
* @return the index of the first position in haplotype1 and haplotype2 where the byte isn't the same
*/
public static int findFirstPositionWhereHaplotypesDiffer(final byte[] haplotype1, final byte[] haplotype2) {
if ( haplotype1 == null || haplotype1.length == 0 ) throw new IllegalArgumentException("Haplotype1 is bad " + haplotype1);
if ( haplotype2 == null || haplotype2.length == 0 ) throw new IllegalArgumentException("Haplotype2 is bad " + haplotype2);
if ( haplotype1 == null || haplotype1.length == 0 ) throw new IllegalArgumentException("Haplotype1 is bad " + Arrays.toString(haplotype1));
if ( haplotype2 == null || haplotype2.length == 0 ) throw new IllegalArgumentException("Haplotype2 is bad " + Arrays.toString(haplotype2));
for( int iii = 0; iii < haplotype1.length && iii < haplotype2.length; iii++ ) {
if( haplotype1[iii] != haplotype2[iii] ) {