diff --git a/heatitup-complete.cabal b/heatitup-complete.cabal
--- a/heatitup-complete.cabal
+++ b/heatitup-complete.cabal
@@ -1,5 +1,5 @@
 name:                heatitup-complete
-version:             0.5.4.0
+version:             0.5.4.1
 synopsis:            Find and annotate ITDs with assembly or read pair joining.
 description:         Find and annotate ITDs with assembly or read pair joining using suffix trees and characterize the exogenous segments within the spacer using heat diffusion.
 homepage:            http://github.com/GregorySchwartz/heatitup-complete#readme
diff --git a/src/Merge.hs b/src/Merge.hs
--- a/src/Merge.hs
+++ b/src/Merge.hs
@@ -88,7 +88,7 @@
 -- supplementary alignments.
 mergePair :: Fill -> [BamRow] -> Maybe BamRow
 mergePair fill xs =
-    case filter (not . isSupplementary) xs of
+    case filter valid xs of
         []  -> Nothing
         [x] -> Just x
         [BamRow left, BamRow right] ->
@@ -103,8 +103,7 @@
     posSeq xs = ( either error (Position . fst) . T.decimal $ xs !! 3
                 , Sequence $ xs !! 9
                 )
-    isSupplementary =
-        (== "1") . drop 11 . decodeSAMFlag . read . T.unpack . (!! 1) . unBamRow
+    valid x = not (checkSamFlag 2048 x) && not (checkSamFlag 256 x)  -- Make sure not supplementary nor not primary
 
 -- | Merge all mate pairs. Assumes that the lines are sorted by mate pair already
 -- (samtools sort -n).
diff --git a/src/Utility.hs b/src/Utility.hs
--- a/src/Utility.hs
+++ b/src/Utility.hs
@@ -15,15 +15,15 @@
     , fastaToMap
     , getMatchMap
     , nub'
-    , decodeSAMFlag
+    , checkSamFlag
     ) where
 
 -- Standard
+import Data.Bits ((.&.))
 import Data.Bool
 import Data.Char
 import Data.Maybe
 import Data.Monoid
-import Numeric
 import qualified Data.ByteString.Char8 as B
 import qualified Data.Map.Strict as Map
 import qualified Data.Set as Set
@@ -31,6 +31,7 @@
 -- Cabal
 import qualified Control.Foldl as Fold
 import qualified Data.Text as T
+import qualified Data.Text.Read as T
 import Data.Fasta.Text
 import Safe
 import Turtle.Line
@@ -100,6 +101,11 @@
 nub' :: (Eq a, Ord a) => [a] -> [a]
 nub' = Set.toList . Set.fromList
 
--- | Decode a SAM flag into the bit representation (as a string).
-decodeSAMFlag :: Int -> String
-decodeSAMFlag x = showIntAtBase 2 intToDigit x ""
+-- | Decode a SAM flag to check a property of the read.
+checkSamFlag :: Int -> BamRow -> Bool
+checkSamFlag property = (== property)
+                      . (.&.) property
+                      . either error fst
+                      . T.decimal
+                      . (!! 1)
+                      . unBamRow