zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

21
public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
View File

@ -60,8 +60,9 @@ public class GATKSAMRecord extends BAMRecord {
private String mReadString = null; private String mReadString = null;
private GATKSAMReadGroupRecord mReadGroup = null; private GATKSAMReadGroupRecord mReadGroup = null;
private byte[] reducedReadCounts = null; private byte[] reducedReadCounts = null;
private int softStart = -1; private final static int UNINITIALIZED = -1;
private int softEnd = -1; private int softStart = UNINITIALIZED;
private int softEnd = UNINITIALIZED;
// because some values can be null, we don't want to duplicate effort // because some values can be null, we don't want to duplicate effort
private boolean retrievedReadGroup = false; 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 * @return the unclipped start of the read taking soft clips (but not hard clips) into account
*/ */
public int getSoftStart() { public int getSoftStart() {
if (softStart < 0) { if ( softStart == UNINITIALIZED ) {
softStart = getAlignmentStart(); softStart = getAlignmentStart();
for (final CigarElement cig : getCigar().getCigarElements()) { for (final CigarElement cig : getCigar().getCigarElements()) {
final CigarOperator op = cig.getOperator(); 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 * @return the unclipped end of the read taking soft clips (but not hard clips) into account
*/ */
public int getSoftEnd() { public int getSoftEnd() {
if ( softEnd < 0 ) { if ( softEnd == UNINITIALIZED ) {
boolean foundAlignedBase = false;
softEnd = getAlignmentEnd(); softEnd = getAlignmentEnd();
final List<CigarElement> cigs = getCigar().getCigarElements(); 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 CigarElement cig = cigs.get(i);
final CigarOperator op = cig.getOperator(); 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(); softEnd += cig.getLength();
else if (op != CigarOperator.HARD_CLIP) else if (op != CigarOperator.HARD_CLIP) {
foundAlignedBase = true;
break; break;
}
}
if( !foundAlignedBase ) { // for example 64H14S, the soft end is actually the same as the alignment end
softEnd = getAlignmentEnd();
} }
} }