diff --git a/umi_tools/sam_methods.py b/umi_tools/sam_methods.py
index 724e1f96..e040d00d 100644
--- a/umi_tools/sam_methods.py
+++ b/umi_tools/sam_methods.py
@@ -589,7 +589,7 @@ def write(self, read, unique_id=None, umi=None, unmapped=False):
             self.write_mates()
             self.chrom = read.reference_name
 
-        key = read.query_name, read.next_reference_name, read.next_reference_start
+        key = read.query_name, read.next_reference_name, read.next_reference_start, read.reference_name, read.reference_start
         self.read1s.add(key)
 
         self.outfile.write(read)
@@ -605,7 +605,7 @@ def write_mates(self):
             if any((read.is_unmapped, read.mate_is_unmapped, read.is_read1)):
                 continue
 
-            key = read.query_name, read.reference_name, read.reference_start
+            key = read.query_name, read.reference_name, read.reference_start, read.next_reference_name, read.next_reference_start
             if key in self.read1s:
                 self.outfile.write(read)
                 self.read1s.remove(key)
@@ -623,10 +623,10 @@ def close(self):
         found = 0
         for read in self.infile.fetch(until_eof=True, multiple_iterators=True):
 
-            if read.is_unmapped:
+            if any((read.is_unmapped, read.mate_is_unmapped, read.is_read1)):
                 continue
 
-            key = read.query_name, read.reference_name, read.reference_start
+            key = read.query_name, read.reference_name, read.reference_start, read.next_reference_name, read.next_reference_start
             if key in self.read1s:
                 self.outfile.write(read)
                 self.read1s.remove(key)