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{-# LANGUAGE ViewPatterns #-}

main = do
  x <- readLn
  let str (if x == 0 then id else const 2 -> y) = show y
  putStrLn (str 1)
{-
$ hpc report Main
100% expressions used (7/7)
100% boolean coverage (0/0)
     100% guards (0/0)
     100% 'if' conditions (0/0)
     100% qualifiers (0/0)
100% alternatives used (0/0)
100% local declarations used (1/1)
100% top-level declarations used (1/1)
-}

{-
Changing str to
  let str z = let y = (if x == 0 then id else const 2) z in show y
results in
$ hpc report Main
 86% expressions used (13/15)
  0% boolean coverage (0/1)
     100% guards (0/0)
       0% 'if' conditions (0/1), 1 always True
     100% qualifiers (0/0)
 50% alternatives used (1/2)
100% local declarations used (2/2)
100% top-level declarations used (1/1)
-}

Specifically, the problem is in addTickMatch and addTickCmdMatch. They are defined like so:

addTickMatch isOneOfMany isLambda match@(Match { m_pats = pats
                                               , m_grhss = gRHSs }) =
  bindLocals (collectPatsBinders pats) $ do
    gRHSs' <- addTickGRHSs isOneOfMany isLambda gRHSs
    return $ match { m_grhss = gRHSs' }

They return the pats as they occurred in the original expression and don't add ticks in the expressions inside them.