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Fixed indexing issue in coordinate conversion 

When a read had been previously soft clipped, the UnclippedEnd could not be used directly as Reference Coordinate for clipping , because the read does not go that far.
This commit is contained in:
Mauricio Carneiro 2011-08-15 01:42:34 -04:00
parent c7b69a4574
commit 489c15b99d
2 changed files with 10 additions and 7 deletions
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11
public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
View File

@ -3,6 +3,7 @@ package org.broadinstitute.sting.utils.clipreads;
import net.sf.samtools.Cigar;
import net.sf.samtools.CigarElement;
import net.sf.samtools.SAMRecord;
import org.broad.tribble.util.PositionalStream;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.jets3t.service.multi.ThreadedStorageService;
@ -48,8 +49,10 @@ public class ReadClipper {
}
public SAMRecord hardClipByReferenceCoordinates(int refStart, int refStop) {
int start = ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStart);
int stop = ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStop);
int start = (refStart < 0) ? 0 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStart);
int stop = (refStop < 0) ? read.getReadLength()-1 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStop);
System.out.println("DEBUG -- clipping start/stop: " + start + "/" + stop);
this.addOp(new ClippingOp(start, stop));
return clipRead(ClippingRepresentation.HARDCLIP_BASES);
}
@ -60,9 +63,9 @@ public class ReadClipper {
}
public SAMRecord hardClipBothEndsByReferenceCoordinates(int left, int right) {
this.read = hardClipByReferenceCoordinates(read.getUnclippedStart(), left);
this.read = hardClipByReferenceCoordinates(-1, left);
this.ops = null; // reset the operations
return hardClipByReferenceCoordinates(right, read.getUnclippedEnd());
return hardClipByReferenceCoordinates(right, -1);
}
/**

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

@ -650,13 +650,13 @@ public class ReadUtils {
return ReadAndIntervalOverlap.RIGHT_OVERLAP;
}
@Requires({"refCoord >= read.getUnclippedStart()", "refCoord <= read.getUnclippedEnd()"})
@Requires({"refCoord >= read.getAlignmentStart()", "refCoord <= read.getAlignmentEnd()"})
@Ensures({"result >= 0", "result < read.getReadLength()"})
public static int getReadCoordinateForReferenceCoordinate(SAMRecord read, int refCoord) {
int readBases = 0;
int refBases = 0;
int goal = refCoord - read.getUnclippedStart(); // read coords are 0-based!
boolean goalReached = false;
int goal = refCoord - read.getAlignmentStart(); // read coords are 0-based!
boolean goalReached = refBases == goal;
Iterator<CigarElement> cigarElementIterator = read.getCigar().getCigarElements().iterator();
while (!goalReached && cigarElementIterator.hasNext()) {