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Bug fix in GATKSAMRecord.getSoftEnd() for reads that are entirely clipped.

This commit is contained in:
Ryan Poplin 2012-10-22 14:21:52 -04:00
parent 90f59803fd
commit 008df54575
1 changed files with 14 additions and 7 deletions
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21
public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
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@ -60,8 +60,9 @@ public class GATKSAMRecord extends BAMRecord {
private String mReadString = null;
private GATKSAMReadGroupRecord mReadGroup = null;
private byte[] reducedReadCounts = null;
private int softStart = -1;
private int softEnd = -1;
private final static int UNINITIALIZED = -1;
private int softStart = UNINITIALIZED;
private int softEnd = UNINITIALIZED;
// because some values can be null, we don't want to duplicate effort
private boolean retrievedReadGroup = false;
@ -386,7 +387,7 @@ public class GATKSAMRecord extends BAMRecord {
* @return the unclipped start of the read taking soft clips (but not hard clips) into account
*/
public int getSoftStart() {
if (softStart < 0) {
if ( softStart == UNINITIALIZED ) {
softStart = getAlignmentStart();
for (final CigarElement cig : getCigar().getCigarElements()) {
final CigarOperator op = cig.getOperator();
@ -408,17 +409,23 @@ public class GATKSAMRecord extends BAMRecord {
* @return the unclipped end of the read taking soft clips (but not hard clips) into account
*/
public int getSoftEnd() {
if ( softEnd < 0 ) {
if ( softEnd == UNINITIALIZED ) {
boolean foundAlignedBase = false;
softEnd = getAlignmentEnd();
final List<CigarElement> cigs = getCigar().getCigarElements();
for (int i=cigs.size() - 1; i>=0; --i) {
for (int i = cigs.size() - 1; i >= 0; --i) {
final CigarElement cig = cigs.get(i);
final CigarOperator op = cig.getOperator();
if (op == CigarOperator.SOFT_CLIP)
if (op == CigarOperator.SOFT_CLIP) // assumes the soft clip that we found is at the end of the aligned read
softEnd += cig.getLength();
else if (op != CigarOperator.HARD_CLIP)
else if (op != CigarOperator.HARD_CLIP) {
foundAlignedBase = true;
break;
}
}
if( !foundAlignedBase ) { // for example 64H14S, the soft end is actually the same as the alignment end
softEnd = getAlignmentEnd();
}
}