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Changing ReadUtils behavior to comply with GenomeLocParser 

Now the functions getRefCoordSoftUnclippedStart and getRefCoordSoftUnclippedEnd will return getUnclippedStart if the read is all contained within an insertion. Updated the contracts accordingly. This should give the same behavior as the GenomeLocParser now.
This commit is contained in:
Mauricio Carneiro 2011-09-19 14:00:00 -04:00
parent 080c957547
commit 56106d54ed
1 changed files with 6 additions and 2 deletions
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8
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; return ReadAndIntervalOverlap.OVERLAP_RIGHT;
} }
@Ensures({"(result >= read.getUnclippedStart() && result <= read.getUnclippedEnd()) || readIsEntirelyInsertion(read)"}) @Ensures({"result >= read.getUnclippedStart()", "result <= read.getUnclippedEnd() || readIsEntirelyInsertion(read)"})
public static int getRefCoordSoftUnclippedStart(SAMRecord read) { public static int getRefCoordSoftUnclippedStart(SAMRecord read) {
int start = read.getUnclippedStart(); int start = read.getUnclippedStart();
for (CigarElement cigarElement : read.getCigar().getCigarElements()) { for (CigarElement cigarElement : read.getCigar().getCigarElements()) {
@ -679,9 +679,13 @@ public class ReadUtils {
return start; return start;
} }
@Ensures({"(result >= read.getUnclippedStart() && result <= read.getUnclippedEnd()) || readIsEntirelyInsertion(read)"}) @Ensures({"result >= read.getUnclippedStart()", "result <= read.getUnclippedEnd() || readIsEntirelyInsertion(read)"})
public static int getRefCoordSoftUnclippedEnd(SAMRecord read) { public static int getRefCoordSoftUnclippedEnd(SAMRecord read) {
int stop = read.getUnclippedStart(); int stop = read.getUnclippedStart();
if (readIsEntirelyInsertion(read))
return stop;
int shift = 0; int shift = 0;
CigarOperator lastOperator = null; CigarOperator lastOperator = null;
for (CigarElement cigarElement : read.getCigar().getCigarElements()) { for (CigarElement cigarElement : read.getCigar().getCigarElements()) {