From 0420591b35b18618c5f307e231faca73ee1d2096 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Torbj=C3=B8rn=20Rognes?= <torognes@ifi.uio.no>
Date: Mon, 1 Mar 2021 17:07:08 +0100
Subject: [PATCH] Remove MIN and MAX macros

---
 src/algo.cc     |  6 +++---
 src/bloompat.cc |  2 +-
 src/nw.cc       |  8 ++++----
 src/swarm.cc    |  6 +++---
 src/swarm.h     | 12 +-----------
 5 files changed, 12 insertions(+), 22 deletions(-)

diff --git a/src/algo.cc b/src/algo.cc
index 3783a048..f5629afa 100644
--- a/src/algo.cc
+++ b/src/algo.cc
@@ -126,9 +126,9 @@ void algo_run(struct Parameters const & p)
     (xmalloc(amplicons * sizeof(uint64_t)));
 
   auto diff_saturation
-    = static_cast<uint64_t>(MIN(UINT8_MAX / penalty_mismatch,
-                                UINT8_MAX / (penalty_gapopen +
-                                       penalty_gapextend)));
+    = static_cast<uint64_t>(std::min(UINT8_MAX / penalty_mismatch,
+                                     UINT8_MAX / (penalty_gapopen +
+                                                  penalty_gapextend)));
 
   unsigned char * dir {nullptr};
   uint64_t * hearray {nullptr};
diff --git a/src/bloompat.cc b/src/bloompat.cc
index f467c8f1..0e307aff 100644
--- a/src/bloompat.cc
+++ b/src/bloompat.cc
@@ -64,7 +64,7 @@ auto bloom_init(uint64_t size) -> struct bloom_s *
 {
   // Size is in bytes for full bitmap, must be power of 2
   // at least 8
-  size = MAX(size, 8);
+  size = std::max(size, static_cast<uint64_t>(8));
 
   auto * b = static_cast<struct bloom_s *>(xmalloc(sizeof(struct bloom_s)));
 
diff --git a/src/nw.cc b/src/nw.cc
index a8d49729..b81697c1 100644
--- a/src/nw.cc
+++ b/src/nw.cc
@@ -165,8 +165,8 @@ void nw(char * dseq,
              +(nt_extract(qseq, static_cast<uint64_t>(i)) + 1)];
 
           dir[index] |= (f < h ? maskup : 0);
-          h = MIN(h, f);
-          h = MIN(h, e);
+          h = std::min(h, f);
+          h = std::min(h, e);
           dir[index] |= (e == h ? maskleft : 0);
 
           *hep = h;
@@ -177,8 +177,8 @@ void nw(char * dseq,
 
           dir[index] |= (f < h ? maskextup : 0);
           dir[index] |= (e < h ? maskextleft : 0);
-          f = MIN(h,f);
-          e = MIN(h,e);
+          f = std::min(h,f);
+          e = std::min(h,e);
 
           *(hep+1) = e;
           h = n;
diff --git a/src/swarm.cc b/src/swarm.cc
index 620ded43..d2084d30 100644
--- a/src/swarm.cc
+++ b/src/swarm.cc
@@ -787,9 +787,9 @@ auto main(int argc, char** argv) -> int
   penalty_gapopen /= penalty_factor;
   penalty_gapextend /= penalty_factor;
 
-  int64_t diff_saturation_16 = (MIN((UINT16_MAX / penalty_mismatch),
-                                    (UINT16_MAX - penalty_gapopen)
-                                    / penalty_gapextend));
+  int64_t diff_saturation_16 = (std::min((UINT16_MAX / penalty_mismatch),
+                                         (UINT16_MAX - penalty_gapopen)
+                                         / penalty_gapextend));
 
   if (p.opt_differences > diff_saturation_16)
     fatal("Resolution (d) too high for the given scoring system");
diff --git a/src/swarm.h b/src/swarm.h
index 148c6614..8d369637 100644
--- a/src/swarm.h
+++ b/src/swarm.h
@@ -39,6 +39,7 @@ constexpr char PRId64[] = "ld";
 #endif
 #endif
 
+#include <algorithm>
 #include <array>
 #include <cassert>
 #include <climits>
@@ -108,19 +109,8 @@ static_assert(INT_MAX > INT16_MAX, "Your compiler uses very short integers.");
 /* constants */
 
 const std::string swarm_version = {"Swarm 3.0.0"};
-// constexpr unsigned int width {32};  // unused?
-// constexpr unsigned int width_shift {5};  // unused?
 constexpr char sepchar {' '};
 constexpr unsigned int bloom_bits_default {16};
-
-#ifndef MIN
-#define MIN(x,y) ((x)<(y)?(x):(y))
-#endif
-
-#ifndef MAX
-#define MAX(x,y) ((x)>(y)?(x):(y))
-#endif
-
 constexpr unsigned int qgramlength {5};
 constexpr unsigned int qgramvectorbits {1 << (2 * qgramlength)};
 constexpr unsigned int qgramvectorbytes {qgramvectorbits / 8};