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Added utility to get the reference coordinate given the read coordinate

This commit is contained in:
Mauricio Carneiro 2012-04-04 16:40:42 -04:00
parent 82cad97caf
commit 1e65474fec
1 changed files with 31 additions and 0 deletions
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31
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
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@ -45,6 +45,10 @@ import java.util.*;
* @version 0.1
*/
public class ReadUtils {
private static final String OFFSET_OUT_OF_BOUNDS_EXCEPTION = "Offset cannot be greater than read length %d : %d";
private static final String OFFSET_NOT_ZERO_EXCEPTION = "We ran past the end of the read and never found the offset, something went wrong!";
private ReadUtils() {
}
@ -748,4 +752,31 @@ public class ReadUtils {
return Arrays.deepToString(sequenceRecordNames);
}
/**
* Calculates the reference coordinate for a read coordinate
*
* @param read the read
* @param offset the base in the read (coordinate in the read)
* @return the reference coordinate correspondent to this base
*/
public static long getReferenceCoordinateForReadCoordinate(GATKSAMRecord read, int offset) {
if (offset > read.getReadLength())
throw new ReviewedStingException(String.format(OFFSET_OUT_OF_BOUNDS_EXCEPTION, offset, read.getReadLength()));
long location = read.getAlignmentStart();
Iterator<CigarElement> cigarElementIterator = read.getCigar().getCigarElements().iterator();
while (offset > 0 && cigarElementIterator.hasNext()) {
CigarElement cigarElement = cigarElementIterator.next();
long move = 0;
if (cigarElement.getOperator().consumesReferenceBases())
move = (long) Math.min(cigarElement.getLength(), offset);
location += move;
offset -= move;
}
if (offset > 0 && !cigarElementIterator.hasNext())
throw new ReviewedStingException(OFFSET_NOT_ZERO_EXCEPTION);
return location;
}
}