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Better exceptions to catch malformed reads 

* throw exceptions in LocusIteratorByState when hitting reads starting or ending with deletions
This commit is contained in:
Mauricio Carneiro 2012-01-31 18:34:53 -05:00
parent 810996cfca
commit 45da892ecc
2 changed files with 11 additions and 4 deletions
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7
public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
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@ -193,6 +193,9 @@ public class LocusIteratorByState extends LocusIterator {
// we reenter in order to re-check cigarElementCounter against curElement's length // we reenter in order to re-check cigarElementCounter against curElement's length
return stepForwardOnGenome(); return stepForwardOnGenome();
} else { } else {
if (curElement != null && curElement.getOperator() == CigarOperator.D)
throw new UserException.MalformedBAM(read, "read ends with deletion. Cigar: " + read.getCigarString());
// Reads that contain indels model the genomeOffset as the following base in the reference. Because // Reads that contain indels model the genomeOffset as the following base in the reference. Because
// we fall into this else block only when indels end the read, increment genomeOffset such that the // we fall into this else block only when indels end the read, increment genomeOffset such that the
// current offset of this read is the next ref base after the end of the indel. This position will // current offset of this read is the next ref base after the end of the indel. This position will
@ -228,7 +231,7 @@ public class LocusIteratorByState extends LocusIterator {
// we see insertions only once, when we step right onto them; the position on the read is scrolled // we see insertions only once, when we step right onto them; the position on the read is scrolled
// past the insertion right after that // past the insertion right after that
if (eventDelayedFlag > 1) if (eventDelayedFlag > 1)
throw new UserException.MalformedBAM(read, "Adjacent I/D events in read " + read.getReadName()); throw new UserException.MalformedBAM(read, String.format("Adjacent I/D events in read %s -- cigar: %s", read.getReadName(), read.getCigarString()));
insertedBases = Arrays.copyOfRange(read.getReadBases(), readOffset + 1, readOffset + 1 + curElement.getLength()); insertedBases = Arrays.copyOfRange(read.getReadBases(), readOffset + 1, readOffset + 1 + curElement.getLength());
eventLength = curElement.getLength(); eventLength = curElement.getLength();
eventStart = readOffset; eventStart = readOffset;
@ -247,7 +250,7 @@ public class LocusIteratorByState extends LocusIterator {
// generate an extended event only if we just stepped into the deletion (i.e. don't // generate an extended event only if we just stepped into the deletion (i.e. don't
// generate the event at every deleted position on the ref, that's what cigarElementCounter==1 is for!) // generate the event at every deleted position on the ref, that's what cigarElementCounter==1 is for!)
if (eventDelayedFlag > 1) if (eventDelayedFlag > 1)
throw new UserException.MalformedBAM(read, "Adjacent I/D events in read " + read.getReadName()); throw new UserException.MalformedBAM(read, String.format("Adjacent I/D events in read %s -- cigar: %s", read.getReadName(), read.getCigarString()));
eventLength = curElement.getLength(); eventLength = curElement.getLength();
eventDelayedFlag = 2; // deletion on the ref causes an immediate return, so we have to delay by 1 only eventDelayedFlag = 2; // deletion on the ref causes an immediate return, so we have to delay by 1 only
eventStart = readOffset; eventStart = readOffset;

8
public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
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@ -4,6 +4,7 @@ import com.google.java.contract.Ensures;
import com.google.java.contract.Requires; import com.google.java.contract.Requires;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
/** /**
@ -146,9 +147,12 @@ public class PileupElement implements Comparable<PileupElement> {
public int getRepresentativeCount() { public int getRepresentativeCount() {
int representativeCount = 1; int representativeCount = 1;
if (read.isReducedRead() && !isInsertionAtBeginningOfRead()) if (read.isReducedRead() && !isInsertionAtBeginningOfRead()) {
representativeCount = (isDeletion()) ? Math.round((read.getReducedCount(offset) + read.getReducedCount(offset + 1)) / 2) : read.getReducedCount(offset); if (isDeletion() && (offset + 1 >= read.getReadLength()) ) // deletion in the end of the read
throw new UserException.MalformedBAM(read, String.format("Adjacent I/D events in read %s -- cigar: %s", read.getReadName(), read.getCigarString()));
representativeCount = (isDeletion()) ? Math.round((read.getReducedCount(offset) + read.getReducedCount(offset + 1)) / 2) : read.getReducedCount(offset);
}
return representativeCount; return representativeCount;
} }