perf: add another fast path to overlap detection

fulcrumgenomics · Sep 27, 2021 · 39fee88 · 39fee88
1 parent 4eaee5e
commit 39fee88
Showing 1 changed file with 1 addition and 0 deletions.
diff --git a/src/main/scala/com/fulcrumgenomics/bam/api/SamRecord.scala b/src/main/scala/com/fulcrumgenomics/bam/api/SamRecord.scala
@@ -193,6 +193,7 @@ trait SamRecord {
   @inline final def matesOverlap: Option[Boolean] = {
     require(mapped && paired && mateMapped, "Cannot determine if mates overlap without paired mates that are both mapped.")
     if (refIndex != mateRefIndex) Some(false)
+    else if (mateStart > end) Some(false)
     else if (mateStart >= start && mateStart <= end) Some(true)
     else mateEnd.map(mateEnd => CoordMath.overlaps(start, end, mateStart, mateEnd))
   }