remove toSimpleInterval()

broadinstitute · Sep 5, 2018 · 28efdce · 28efdce
1 parent 139e12d
commit 28efdce
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Showing 2 changed files with 4 additions and 10 deletions.
diff --git a/...ain/java/org/broadinstitute/hellbender/tools/spark/sv/evidence/XGBoostEvidenceFilter.java b/...ain/java/org/broadinstitute/hellbender/tools/spark/sv/evidence/XGBoostEvidenceFilter.java
@@ -417,7 +417,10 @@ private static class CigarQualityInfo {
     private static double getGenomeIntervalsOverlap(final BreakpointEvidence evidence,
                                                     final FeatureDataSource<BEDFeature> genomeIntervals,
                                                     final ReadMetadata readMetadata) {
-        final SimpleInterval simpleInterval = evidence.getLocation().toSimpleInterval(readMetadata);
+        final SVInterval location = evidence.getLocation();
+        final SimpleInterval simpleInterval = new SimpleInterval(readMetadata.getContigName(location.getContig()),
+                location.getStart(),
+                location.getEnd() - 1); // "end - 1" because SimpleIntervals are closed on both ends
         int overlap = 0;
         for(final Iterator<BEDFeature> overlapperItr = genomeIntervals.query(simpleInterval); overlapperItr.hasNext();) {
             final BEDFeature overlapper = overlapperItr.next();

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/utils/SVInterval.java b/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/utils/SVInterval.java
@@ -43,10 +43,6 @@ public final class SVInterval implements Comparable<SVInterval> {
     private final int start;
     private final int end;
 
-    /**
-     * Note: according to {@link #toBedString(ReadMetadata)} and {@link #toSimpleInterval(ReadMetadata)},
-     * {@code start} should be on a 1-based coordinate system, rather than 0-based.
-     */
     public SVInterval( final int contig, final int start, final int end ) {
         this.contig = contig;
         this.start = start;
@@ -153,11 +149,6 @@ public int compareTo( final SVInterval that ) {
         return result;
     }
 
-    public SimpleInterval toSimpleInterval(final ReadMetadata readMetadata) {
-        // "end - 1" because SimpleIntervals are closed on both ends
-        return new SimpleInterval(readMetadata.getContigName(contig), start, end - 1);
-    }
-
     @Override
     public String toString() { return Integer.toString(contig)+"["+start+":"+end+"]"; }