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Cleaning up hilarious exception messages 

Too many users (with RNASeq reads) are hitting these exceptions that were never supposed to happen. Let's give them (and us) a better and clearer error message.
This commit is contained in:
Mauricio Carneiro 2013-03-04 16:47:45 -05:00
parent ce7554e9d6
commit d0c8105387
2 changed files with 5 additions and 5 deletions
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4
public/java/src/org/broadinstitute/sting/utils/clipping/ReadClipper.java
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@ -28,8 +28,8 @@ package org.broadinstitute.sting.utils.clipping;
import com.google.java.contract.Requires;
import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator;
import org.broadinstitute.sting.utils.recalibration.EventType;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.recalibration.EventType;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
@ -534,7 +534,7 @@ public class ReadClipper {
throw new ReviewedStingException("Trying to clip before the start or after the end of a read");
if ( start > stop )
throw new ReviewedStingException(String.format("START (%d) > (%d) STOP -- this should never happen -- call Mauricio!", start, stop));
throw new ReviewedStingException(String.format("START (%d) > (%d) STOP -- this should never happen, please check read: %s (CIGAR: %s)", start, stop, read, read.getCigarString()));
if ( start > 0 && stop < read.getReadLength() - 1)
throw new ReviewedStingException(String.format("Trying to clip the middle of the read: start %d, stop %d, cigar: %s", start, stop, read.getCigarString()));

6
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
View File

@ -29,12 +29,12 @@ import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
import net.sf.samtools.*;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.NGSPlatform;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.BaseUtils;
import java.io.File;
import java.util.*;
@ -485,7 +485,7 @@ public class ReadUtils {
if (allowGoalNotReached) {
return new Pair<Integer, Boolean>(CLIPPING_GOAL_NOT_REACHED, false);
} else {
throw new ReviewedStingException("Reference coordinate corresponds to a non-existent base in the read. This should never happen -- call Mauricio");
throw new ReviewedStingException(String.format("Reference coordinate corresponds to a non-existent base in the read. This should never happen -- check read with alignment start: %s and cigar: %s", alignmentStart, cigar));
}
}
@ -506,7 +506,7 @@ public class ReadUtils {
if (allowGoalNotReached) {
return new Pair<Integer, Boolean>(CLIPPING_GOAL_NOT_REACHED, false);
} else {
throw new ReviewedStingException("Reference coordinate corresponds to a non-existent base in the read. This should never happen -- call Mauricio");
throw new ReviewedStingException(String.format("Reference coordinate corresponds to a non-existent base in the read. This should never happen -- check read with alignment start: %s and cigar: %s", alignmentStart, cigar));
}
}