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Fixed second time clipping 

When a read is clipped once, and then in the second operation, because of indels, it doesn't reach the coordinate initially set for hard clipping, the indices were wrong. This should fix it.
This commit is contained in:
Mauricio Carneiro 2011-08-15 12:04:53 -04:00
parent 489c15b99d
commit 0d976d6211
2 changed files with 5 additions and 5 deletions
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2
public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
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@ -50,7 +50,7 @@ public class ReadClipper {
public SAMRecord hardClipByReferenceCoordinates(int refStart, int refStop) { public SAMRecord hardClipByReferenceCoordinates(int refStart, int refStop) {
int start = (refStart < 0) ? 0 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStart); int start = (refStart < 0) ? 0 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStart);
int stop = (refStop < 0) ? read.getReadLength()-1 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStop); int stop = (refStop < 0) ? read.getReadLength() - 1 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStop);
System.out.println("DEBUG -- clipping start/stop: " + start + "/" + stop); System.out.println("DEBUG -- clipping start/stop: " + start + "/" + stop);
this.addOp(new ClippingOp(start, stop)); this.addOp(new ClippingOp(start, stop));

8
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
View File

@ -655,16 +655,16 @@ public class ReadUtils {
public static int getReadCoordinateForReferenceCoordinate(SAMRecord read, int refCoord) { public static int getReadCoordinateForReferenceCoordinate(SAMRecord read, int refCoord) {
int readBases = 0; int readBases = 0;
int refBases = 0; int refBases = 0;
int goal = refCoord - read.getAlignmentStart(); // read coords are 0-based! int goal = refCoord - read.getAlignmentStart(); // The goal is to move this many reference bases
boolean goalReached = refBases == goal; boolean goalReached = refBases == goal;
Iterator<CigarElement> cigarElementIterator = read.getCigar().getCigarElements().iterator(); Iterator<CigarElement> cigarElementIterator = read.getCigar().getCigarElements().iterator();
while (!goalReached && cigarElementIterator.hasNext()) { while (!goalReached && cigarElementIterator.hasNext()) {
CigarElement cigarElement = cigarElementIterator.next(); CigarElement cigarElement = cigarElementIterator.next();
int shift = 0; int shift = 0;
if (refBases == 0 && readBases == 0 && cigarElement.getOperator() == CigarOperator.HARD_CLIP) { //if (refBases == 0 && readBases == 0 && cigarElement.getOperator() == CigarOperator.HARD_CLIP) {
goal -= cigarElement.getLength(); // goal -= cigarElement.getLength();
} //}
if (cigarElement.getOperator().consumesReferenceBases()) { if (cigarElement.getOperator().consumesReferenceBases()) {
if (refBases + cigarElement.getLength() < goal) { if (refBases + cigarElement.getLength() < goal) {