zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

8
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
View File

@ -667,7 +667,7 @@ public class ReadUtils {
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) {
int start = read.getUnclippedStart();
for (CigarElement cigarElement : read.getCigar().getCigarElements()) {
@ -679,9 +679,13 @@ public class ReadUtils {
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) {
int stop = read.getUnclippedStart();
if (readIsEntirelyInsertion(read))
return stop;
int shift = 0;
CigarOperator lastOperator = null;
for (CigarElement cigarElement : read.getCigar().getCigarElements()) {