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Fixing contracts for SoftUnclippedEnd utils 

Now accepts reads that are entirely contained inside an insertion.
This commit is contained in:
Mauricio Carneiro 2011-09-19 13:53:08 -04:00
parent ba150570f3
commit 080c957547
1 changed files with 10 additions and 2 deletions
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12
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
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@ -667,7 +667,7 @@ public class ReadUtils {
return ReadAndIntervalOverlap.OVERLAP_RIGHT;
}
@Ensures({"result >= read.getUnclippedStart()", "result <= read.getUnclippedEnd()"})
@Ensures({"(result >= read.getUnclippedStart() && result <= read.getUnclippedEnd()) || readIsEntirelyInsertion(read)"})
public static int getRefCoordSoftUnclippedStart(SAMRecord read) {
int start = read.getUnclippedStart();
for (CigarElement cigarElement : read.getCigar().getCigarElements()) {
@ -679,7 +679,7 @@ public class ReadUtils {
return start;
}
@Ensures({"result >= read.getUnclippedStart()", "result <= read.getUnclippedEnd()"})
@Ensures({"(result >= read.getUnclippedStart() && result <= read.getUnclippedEnd()) || readIsEntirelyInsertion(read)"})
public static int getRefCoordSoftUnclippedEnd(SAMRecord read) {
int stop = read.getUnclippedStart();
int shift = 0;
@ -695,6 +695,14 @@ public class ReadUtils {
return (lastOperator == CigarOperator.HARD_CLIP) ? stop-1 : stop+shift-1 ;
}
private static boolean readIsEntirelyInsertion(SAMRecord read) {
for (CigarElement cigarElement : read.getCigar().getCigarElements()) {
if (cigarElement.getOperator() != CigarOperator.INSERTION)
return false;
}
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.