Restore consensus calling for pairs with only one mapped read.

fulcrumgenomics · Oct 31, 2023 · a5a41b6 · a5a41b6
1 parent 6fa1fde
commit a5a41b6
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/src/main/scala/com/fulcrumgenomics/umi/ConsensusCallingIterator.scala b/src/main/scala/com/fulcrumgenomics/umi/ConsensusCallingIterator.scala
@@ -53,9 +53,9 @@ class ConsensusCallingIterator[ConsensusRead <: SimpleRead](sourceIterator: Iter
   private var collectedStats: Boolean = false
 
   protected val iter: Iterator[SamRecord] = {
-    val filteredIterator = sourceIterator.filterNot { r =>
-      r.secondary || r.supplementary || r.unmapped || (r.paired && r.mateUnmapped)
-    }
+    val filteredIterator = sourceIterator
+      .filterNot (r => r.secondary || r.supplementary)
+      .filter(r => r.mapped || (r.paired && r.mateMapped))
 
     // Wrap our input iterator in a progress logging iterator if we have a progress logger
     val progressIterator = progress match {