From a5a41b68a404e5f147951b2f987c32e9f46a0336 Mon Sep 17 00:00:00 2001
From: tfenne <tfenne@tfenne.com>
Date: Tue, 31 Oct 2023 08:45:34 -0600
Subject: [PATCH] Restore consensus calling for pairs with only one mapped
 read.

---
 .../com/fulcrumgenomics/umi/ConsensusCallingIterator.scala  | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/main/scala/com/fulcrumgenomics/umi/ConsensusCallingIterator.scala b/src/main/scala/com/fulcrumgenomics/umi/ConsensusCallingIterator.scala
index d99c7559c..17b68df87 100644
--- 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 {