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Bug fixes with Mauricio to functions in ReadUtils used by reduced reads and the haplotype caller.

This commit is contained in:
Ryan Poplin 2011-11-02 16:29:10 -04:00
parent 74b018a1f3
commit 4d35272916
1 changed files with 55 additions and 98 deletions
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51
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
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@ -726,38 +726,6 @@ public class ReadUtils {
return true; return true;
} }
/**
* Looks for a read coordinate that corresponds to the reference coordinate in the soft clipped region before
* the alignment start of the read.
*
* @param read
* @param refCoord
* @return the corresponding read coordinate or -1 if it failed to find it (it has been hard clipped before)
*/
@Requires({"refCoord >= read.getUnclippedStart()", "refCoord < read.getAlignmentStart()"})
private static int getReadCoordinateForReferenceCoordinateBeforeAlignmentStart(SAMRecord read, int refCoord) {
if (getRefCoordSoftUnclippedStart(read) <= refCoord)
return refCoord - getRefCoordSoftUnclippedStart(read) + 1;
return -1;
}
/**
* Looks for a read coordinate that corresponds to the reference coordinate in the soft clipped region after
* the alignment end of the read.
*
* @param read
* @param refCoord
* @return the corresponding read coordinate or -1 if it failed to find it (it has been hard clipped before)
*/
@Requires({"refCoord <= read.getUnclippedEnd()", "refCoord > read.getAlignmentEnd()"})
private static int getReadCoordinateForReferenceCoordinateBeforeAlignmentEnd(SAMRecord read, int refCoord) {
if (getRefCoordSoftUnclippedEnd(read) >= refCoord)
return refCoord - getRefCoordSoftUnclippedStart(read) + 1;
return -1;
}
public enum ClippingTail { public enum ClippingTail {
LEFT_TAIL, LEFT_TAIL,
RIGHT_TAIL RIGHT_TAIL
@ -802,25 +770,14 @@ public class ReadUtils {
* @param refCoord * @param refCoord
* @return the read coordinate corresponding to the requested reference coordinate. (see warning!) * @return the read coordinate corresponding to the requested reference coordinate. (see warning!)
*/ */
@Requires({"refCoord >= read.getUnclippedStart()", "refCoord <= read.getUnclippedEnd()"}) @Requires({"refCoord >= getRefCoordSoftUnclippedStart(read)", "refCoord <= getRefCoordSoftUnclippedEnd(read)"})
@Ensures({"result.getFirst() >= 0", "result.getFirst() < read.getReadLength()"}) @Ensures({"result.getFirst() >= 0", "result.getFirst() < read.getReadLength()"})
public static Pair<Integer, Boolean> getReadCoordinateForReferenceCoordinate(SAMRecord read, int refCoord) { public static Pair<Integer, Boolean> getReadCoordinateForReferenceCoordinate(SAMRecord read, int refCoord) {
int readBases = 0; int readBases = 0;
int refBases = 0; int refBases = 0;
boolean fallsInsideDeletion = false; boolean fallsInsideDeletion = false;
if (refCoord < read.getAlignmentStart()) { int goal = refCoord - getRefCoordSoftUnclippedStart(read); // The goal is to move this many reference bases
readBases = getReadCoordinateForReferenceCoordinateBeforeAlignmentStart(read, refCoord);
if (readBases < 0)
throw new ReviewedStingException("Requested a coordinate in a hard clipped area of the read. No equivalent read coordinate.");
}
else if (refCoord > read.getAlignmentEnd()) {
readBases = getReadCoordinateForReferenceCoordinateBeforeAlignmentEnd(read, refCoord);
if (readBases < 0)
throw new ReviewedStingException("Requested a coordinate in a hard clipped area of the read. No equivalent read coordinate.");
}
else {
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();
@ -828,7 +785,7 @@ public class ReadUtils {
CigarElement cigarElement = cigarElementIterator.next(); CigarElement cigarElement = cigarElementIterator.next();
int shift = 0; int shift = 0;
if (cigarElement.getOperator().consumesReferenceBases()) { if (cigarElement.getOperator().consumesReferenceBases() || cigarElement.getOperator() == CigarOperator.SOFT_CLIP) {
if (refBases + cigarElement.getLength() < goal) if (refBases + cigarElement.getLength() < goal)
shift = cigarElement.getLength(); shift = cigarElement.getLength();
else else
@ -891,7 +848,7 @@ public class ReadUtils {
if (!goalReached) if (!goalReached)
throw new ReviewedStingException("Somehow the requested coordinate is not covered by the read. Too many deletions?"); throw new ReviewedStingException("Somehow the requested coordinate is not covered by the read. Too many deletions?");
}
return new Pair<Integer, Boolean>(readBases, fallsInsideDeletion); return new Pair<Integer, Boolean>(readBases, fallsInsideDeletion);
} }