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Uses the cleaner new GenomeLoc(read) syntax 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@393 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-04-14 00:53:58 +00:00
parent 11377ef390
commit cc75e8f712
3 changed files with 5 additions and 5 deletions
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4
java/src/org/broadinstitute/sting/gatk/iterators/SortSamIterator.java
View File

@ -53,8 +53,8 @@ public class SortSamIterator implements Iterator<SAMRecord> {
}
public int compareTo(ComparableSAMRecord o) {
GenomeLoc myLoc = GenomeLoc.genomicLocationOf(record);
GenomeLoc hisLoc = GenomeLoc.genomicLocationOf(o.getRecord());
GenomeLoc myLoc = new GenomeLoc(record);
GenomeLoc hisLoc = new GenomeLoc(o.getRecord());
return myLoc.compareTo(hisLoc);
}
}

4
java/src/org/broadinstitute/sting/gatk/iterators/VerifyingSamIterator.java
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@ -55,8 +55,8 @@ public class VerifyingSamIterator implements Iterator<SAMRecord> {
if ( last == null || cur.getReadUnmappedFlag() )
return false;
else {
GenomeLoc lastLoc = GenomeLoc.genomicLocationOf( last );
GenomeLoc curLoc = GenomeLoc.genomicLocationOf( cur );
GenomeLoc lastLoc = new GenomeLoc( last );
GenomeLoc curLoc = new GenomeLoc( cur );
return curLoc.compareTo(lastLoc) == -1;
}
}

2
java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java
View File

@ -81,7 +81,7 @@ public class TraverseByReads extends TraversalEngine {
// get the next read
final SAMRecord read = samReadIter.next();
final List<SAMRecord> reads = Arrays.asList(read);
GenomeLoc loc = GenomeLoc.genomicLocationOf(read);
GenomeLoc loc = new GenomeLoc(read);
// Jump forward in the reference to this locus location
LocusContext locus = new LocusContext(loc, reads, offsets);