From 95661ae45143a4fd12428d5f34230c1479cddc10 Mon Sep 17 00:00:00 2001
From: Andrew D Smith <andrewds@usc.edu>
Date: Tue, 3 Mar 2026 15:28:36 -0800
Subject: [PATCH 01/11] src/html_template.hpp: changing the version string in
 the html template to take value from project config

---
 src/html_template.hpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/html_template.hpp b/src/html_template.hpp
index 71308d8..c016b4b 100644
--- a/src/html_template.hpp
+++ b/src/html_template.hpp
@@ -389,7 +389,7 @@ p {
 
 
 </div>
-<div class="footer">Falco 1.2.5
+<div class="footer">Falco {{version}}
 </div>
 </body>
 <script src="https://code.jquery.com/jquery-3.3.1.slim.min.js" 

From 41dfb175f4b8b0d63b5f1d83f944473c7dd176ab Mon Sep 17 00:00:00 2001
From: Andrew D Smith <andrewds@usc.edu>
Date: Tue, 3 Mar 2026 15:29:08 -0800
Subject: [PATCH 02/11] src/falco.cpp: taking VERSION from the config.h

---
 src/falco.cpp | 25 ++++++++++++-------------
 1 file changed, 12 insertions(+), 13 deletions(-)

diff --git a/src/falco.cpp b/src/falco.cpp
index 2f21148..30702a8 100644
--- a/src/falco.cpp
+++ b/src/falco.cpp
@@ -15,20 +15,24 @@
  * General Public License for more details.
  */
 
-#include <chrono>
-#include <filesystem>
-#include <fstream>
-#include <string>
-#include <vector>
 
 #include "FalcoConfig.hpp"
 #include "FastqStats.hpp"
 #include "HtmlMaker.hpp"
 #include "Module.hpp"
+
 #include "OptionParser.hpp"
 #include "StreamReader.hpp"
 #include "smithlab_utils.hpp"
 
+#include "config.h"
+
+#include <chrono>
+#include <filesystem>
+#include <fstream>
+#include <string>
+#include <vector>
+
 // Function to get seconds elapsed in program
 static std::size_t
 get_seconds_since(
@@ -162,7 +166,7 @@ write_results(const FalcoConfig &falco_config, FastqStats &stats,
       log_process("Writing text report to " + qc_data_file);
 
     // put header
-    qc_data_txt << "##Falco\t" + FalcoConfig::FalcoVersion + "\n";
+    qc_data_txt << "##Falco\t" + std::string{VERSION} + "\n";
     if (do_call)
       qc_data_txt << "##Call\t" << falco_config.call << "\n";
   }
@@ -262,17 +266,12 @@ write_results(const FalcoConfig &falco_config, FastqStats &stats,
     html << html_maker.html_boilerplate;
 }
 
-[[nodiscard]] inline bool
-file_exists(const std::string &file_name) {
-  return access(file_name.data(), F_OK) == 0;
-}
-
 int
 main(int argc, char *argv[]) {
 
   try {
     static const std::string FALCO_VERSION =
-      "falco " + FalcoConfig::FalcoVersion;
+      "falco " + std::string{VERSION};
     bool help = false;
     bool version = false;
 
@@ -633,7 +632,7 @@ main(int argc, char *argv[]) {
     // check if all filenames exist
     bool all_files_exist = true;
     for (std::size_t i = 0; i < std::size(all_seq_filenames); ++i) {
-      if (!file_exists(all_seq_filenames[i])) {
+      if (!std::filesystem::exists(all_seq_filenames[i])) {
         std::cerr << "ERROR! File does not exist: " << all_seq_filenames[i]
                   << '\n';
         all_files_exist = false;

From 4dc8148c6387d7e91f04255ab63c6a7c3077f759 Mon Sep 17 00:00:00 2001
From: Andrew D Smith <andrewds@usc.edu>
Date: Tue, 3 Mar 2026 15:29:25 -0800
Subject: [PATCH 03/11] src/FalcoConfig.cpp: taking VERSION from the config.h

---
 src/FalcoConfig.cpp | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/FalcoConfig.cpp b/src/FalcoConfig.cpp
index d4dfbfb..1d855e3 100644
--- a/src/FalcoConfig.cpp
+++ b/src/FalcoConfig.cpp
@@ -17,6 +17,8 @@
 #include "FastqStats.hpp"
 #include "html_template.hpp"
 
+#include "config.h"
+
 #include <sys/stat.h>
 #include <unistd.h>
 
@@ -25,7 +27,7 @@
 #include <fstream>
 #include <sstream>
 
-const std::string FalcoConfig::FalcoVersion = "1.2.5";
+const std::string FalcoConfig::FalcoVersion = VERSION;
 
 /*********************************************************/
 /************** DEFAULT VALUES FOR FILES *****************/

From 4ac80f9dcdd9bb1fe5bdaf1d242c2d3116e06663 Mon Sep 17 00:00:00 2001
From: Andrew D Smith <andrewds@usc.edu>
Date: Tue, 3 Mar 2026 15:30:22 -0800
Subject: [PATCH 04/11] configure.ac: defining PROGRAM_PATH from configure.ac
 instead of Makefile.am

---
 configure.ac | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/configure.ac b/configure.ac
index d527ac1..746565e 100644
--- a/configure.ac
+++ b/configure.ac
@@ -31,6 +31,9 @@ AS_IF([test "x$CXXFLAGS_set" != "xset"], [
 ])
 AC_MSG_NOTICE([CXXFLAGS is $CXXFLAGS])
 
+AC_DEFINE_UNQUOTED([PROGRAM_PATH], ["$srcdir"],
+  [The PROGRAM_PATH variable])
+
 AX_CXX_COMPILE_STDCXX_17([noext], [mandatory])
 AC_OPENMP([C++]) dnl make sure we have openmp for multi-core in falco
 

From 6bcd7867b78643697343166902e8d837d0403427 Mon Sep 17 00:00:00 2001
From: Andrew D Smith <andrewds@usc.edu>
Date: Tue, 3 Mar 2026 16:04:10 -0800
Subject: [PATCH 05/11] src/HtmlMaker.cpp: getting version from config.h and
 using regex to replace strings in the html template

---
 src/HtmlMaker.cpp | 39 +++++++++++++++++++++++----------------
 1 file changed, 23 insertions(+), 16 deletions(-)

diff --git a/src/HtmlMaker.cpp b/src/HtmlMaker.cpp
index 3652ac0..1dc8ca6 100644
--- a/src/HtmlMaker.cpp
+++ b/src/HtmlMaker.cpp
@@ -15,10 +15,13 @@
 
 #include "HtmlMaker.hpp"
 
+#include "config.h"
+
 #include <algorithm>
 #include <chrono>
 #include <fstream>
 #include <sstream>
+#include <regex>
 
 void
 HtmlMaker::put_data(const std::string &placeholder, const std::string &data) {
@@ -29,7 +32,7 @@ HtmlMaker::put_data(const std::string &placeholder, const std::string &data) {
 
   // at least one placeholder found
   while (pos != std::string::npos) {
-    html_boilerplate.replace(pos, placeholder.size(), data);
+    html_boilerplate.replace(pos, std::size(placeholder), data);
     pos = html_boilerplate.find(placeholder, pos + 1);
   }
 }
@@ -37,15 +40,12 @@ HtmlMaker::put_data(const std::string &placeholder, const std::string &data) {
 // Comments out html pieces if analyses were skipped
 void
 HtmlMaker::put_comment(std::string &comment_begin, std::string &comment_end,
-                       bool done) {
-  // put html comments if analysis was skipped
-  if (!done) {
+                       const bool done) {
+  if (!done) { // put html comments if analysis was skipped
     put_data(comment_begin, "<!--");
     put_data(comment_end, "-->");
   }
-
-  // otherwise delete placeholder
-  else {
+  else { // otherwise delete placeholder
     put_data(comment_begin, "");
     put_data(comment_end, "");
   }
@@ -53,14 +53,21 @@ HtmlMaker::put_comment(std::string &comment_begin, std::string &comment_end,
 
 void
 HtmlMaker::put_file_details(const FalcoConfig &falco_config) {
-  // Put file name in filename placeholder
-  put_data("{{filename}}", falco_config.filename_stripped);
+  using namespace std::string_literals;
+  static const auto left_tag = "\\{\\{"s;
+  static const auto right_tag = "\\}\\}"s;
 
-  // Put date on date placeholder
-  auto tmp =
-    std::chrono::system_clock::to_time_t(std::chrono::system_clock::now());
-  std::string time_fmt = std::string(ctime(&tmp));
-  put_data("{{date}}", time_fmt);
-}
+  std::regex filename_re(left_tag + "filename"s + right_tag);
+  std::regex_replace(html_boilerplate, filename_re,
+                     falco_config.filename_stripped);
 
-HtmlMaker::HtmlMaker() { html_boilerplate = FalcoConfig::html_template; }
+  using system_clock = std::chrono::system_clock;
+  auto time_unformatted = system_clock::to_time_t(system_clock::now());
+  std::string time_formatted = std::string(ctime(&time_unformatted));
+
+  std::regex date_re(left_tag + "date"s + right_tag);
+  std::regex_replace(html_boilerplate, date_re, time_formatted);
+
+  std::regex version_re(left_tag + "version"s + right_tag);
+  std::regex_replace(html_boilerplate, version_re, VERSION);
+}

From 286e6226d93c70e41837eea95464f1f672757443 Mon Sep 17 00:00:00 2001
From: Andrew D Smith <andrewds@usc.edu>
Date: Tue, 3 Mar 2026 16:05:14 -0800
Subject: [PATCH 06/11] src/HtmlMaker.hpp: putting constructor definition in
 the header with declaration

---
 src/HtmlMaker.hpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/HtmlMaker.hpp b/src/HtmlMaker.hpp
index becc3a5..d0283a0 100644
--- a/src/HtmlMaker.hpp
+++ b/src/HtmlMaker.hpp
@@ -28,7 +28,7 @@
 class HtmlMaker {
 public:
   std::string html_boilerplate;
-  HtmlMaker();
+  HtmlMaker() : html_boilerplate{FalcoConfig::html_template} {}
   // Fill data from module
   void put_data(const std::string &placeholder, const std::string &data);
 

From 5a5687e3f90dcd77e47ae7e092c0fb12a11edbfe Mon Sep 17 00:00:00 2001
From: Andrew D Smith <andrewds@usc.edu>
Date: Tue, 3 Mar 2026 16:11:18 -0800
Subject: [PATCH 07/11] src/HtmlMaker.hpp: added forgotten const

---
 src/HtmlMaker.hpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/HtmlMaker.hpp b/src/HtmlMaker.hpp
index d0283a0..80f9914 100644
--- a/src/HtmlMaker.hpp
+++ b/src/HtmlMaker.hpp
@@ -35,7 +35,7 @@ class HtmlMaker {
   // Comment or remove placeholders
   void put_comment(std::string &comment_begin,
                    std::string &comment_end,
-                   bool done);
+                   const bool done);
 
   // Put file details and date
   void put_file_details(const FalcoConfig &falco_config);

From dd5e47cefc78d0755c6cfb07958e7f20ac78e8e4 Mon Sep 17 00:00:00 2001
From: Andrew D Smith <andrewds@usc.edu>
Date: Tue, 3 Mar 2026 16:44:16 -0800
Subject: [PATCH 08/11] Makefile and src/Makefile: removing these and requiring
 Makefiles to come from automake

---
 Makefile     | 27 --------------------------
 src/Makefile | 54 ----------------------------------------------------
 2 files changed, 81 deletions(-)
 delete mode 100644 Makefile
 delete mode 100644 src/Makefile

diff --git a/Makefile b/Makefile
deleted file mode 100644
index 82b5c9f..0000000
--- a/Makefile
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright (C) 2019-2020 Guilherme de Sena Brandine
-#
-# Authors: Andrew D. Smith
-#
-# This file is part of ABISMAL.
-#
-# ABISMAL is free software: you can redistribute it and/or modify it
-# under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# ABISMAL is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
-# or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public
-# License for more details.
-#
-
-SRC_ROOT=$(shell pwd)
-all:
-	@make -C src SRC_ROOT=$(SRC_ROOT) all
-
-install:
-	@make -C src SRC_ROOT=$(SRC_ROOT) install
-
-clean:
-	@make -C src clean
-.PHONY: clean
diff --git a/src/Makefile b/src/Makefile
deleted file mode 100644
index 71d3428..0000000
--- a/src/Makefile
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright (C) 2018-2019 Andrew D. Smith
-#
-# Authors: Andrew D. Smith
-#
-# This file is part of ABISMAL.
-#
-# ABISMAL is free software: you can redistribute it and/or modify it
-# under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# ABISMAL is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
-# or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public
-# License for more details.
-
-PROGS = falco
-
-CXX = g++
-CXXFLAGS = -Wall -std=c++11
-CPPFLAGS = -DPROGRAM_PATH=\"$(SRC_ROOT)\"
-LDLIBS = -lz
-OPTFLAGS = -O3
-DEBUGFLAGS = -g
-
-ifdef HAVE_HTSLIB
-CPPFLAGS += -DUSE_HTS
-LDLIBS += -lhts
-endif
-
-ifdef DEBUG
-CXXFLAGS += $(DEBUGFLAGS)
-else
-CXXFLAGS += $(OPTFLAGS)
-endif
-
-all: $(PROGS)
-install: $(PROGS)
-	@mkdir -p $(SRC_ROOT)/bin
-	@install -m 755 $(PROGS) $(SRC_ROOT)/bin
-
-%.o: %.cpp %.hpp
-	$(CXX) $(CXXFLAGS) -c -o $@ $< $(CPPFLAGS)
-
-$(PROGS): FalcoConfig.o FastqStats.o HtmlMaker.o Module.o OptionParser.o \
-	        smithlab_utils.o StreamReader.o
-
-%: %.cpp
-	$(CXX) $(CXXFLAGS) -o $@ $^ $(CPPFLAGS) $(LDLIBS)
-
-clean:
-	@-rm -f $(PROGS) *.o *.so *.a *~
-.PHONY: clean
-

From 5302c38d223a0f637e7d1ddc6501ddd9611ceb01 Mon Sep 17 00:00:00 2001
From: Andrew D Smith <andrewds@usc.edu>
Date: Tue, 3 Mar 2026 16:47:49 -0800
Subject: [PATCH 09/11] configure.ac: removing the OPENMP stuff as it seems not
 used

---
 configure.ac | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/configure.ac b/configure.ac
index 746565e..d9a8b9a 100644
--- a/configure.ac
+++ b/configure.ac
@@ -35,7 +35,7 @@ AC_DEFINE_UNQUOTED([PROGRAM_PATH], ["$srcdir"],
   [The PROGRAM_PATH variable])
 
 AX_CXX_COMPILE_STDCXX_17([noext], [mandatory])
-AC_OPENMP([C++]) dnl make sure we have openmp for multi-core in falco
+dnl AC_OPENMP([C++]) dnl make sure we have openmp for multi-core in falco
 
 dnl check for the Zlib library
 AC_CHECK_LIB([z], [zlibVersion], [],

From c833d8a255d3ffa180f2b2be35a922b2d7bbea0b Mon Sep 17 00:00:00 2001
From: Andrew D Smith <andrewds@usc.edu>
Date: Tue, 3 Mar 2026 16:48:17 -0800
Subject: [PATCH 10/11] Makefile.am: attempting to simplify

---
 Makefile.am | 20 ++++++++------------
 1 file changed, 8 insertions(+), 12 deletions(-)

diff --git a/Makefile.am b/Makefile.am
index 46a242b..8ffc954 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -17,22 +17,16 @@
 EXTRA_DIST = README.md LICENSE Configuration example.fq test
 
 ACLOCAL_AMFLAGS = -I m4
-AM_CPPFLAGS = -I $(top_srcdir)/src
 
-### ADS: use AM_CXXFLAGS if these are needed
-## AM_CXXFLAGS = -Wall -Wextra -Wpedantic -Wno-unknown-attributes
-
-TESTS = test/falco.test
-TEST_EXTENSIONS = .test
-
-bin_PROGRAMS = falco
-
-falco_CXXFLAGS = $(OPENMP_CXXFLAGS) $(AM_CXXFLAGS)
-falco_CPPFLAGS = -DPROGRAM_PATH=\"$(abspath $(top_srcdir))\"
+# ADS: fix the order of user and project set vars; shouldn't need to worry about
+# setting CXXFLAGS in configure.ac
+AM_CXXFLAGS = -Wall -Wextra -Wpedantic
 if ENABLE_HTS
-falco_CPPFLAGS += -DUSE_HTS
+CPPFLAGS += -DUSE_HTS
 endif
 
+bin_PROGRAMS = falco
+
 falco_SOURCES = \
 	src/falco.cpp \
 	src/FastqStats.cpp \
@@ -52,4 +46,6 @@ falco_SOURCES = \
 	src/smithlab_utils.hpp \
 	src/aux.hpp
 
+TESTS = test/falco.test
+TEST_EXTENSIONS = .test
 CLEANFILES = tests_build/test_data.tgz

From e25fe85c9dba2da38de173370703600f7d73a7f6 Mon Sep 17 00:00:00 2001
From: Andrew D Smith <andrewds@usc.edu>
Date: Tue, 3 Mar 2026 16:48:50 -0800
Subject: [PATCH 11/11] src/smithlab_utils.hpp: trying to speedup the
 kmer_counts function

---
 src/smithlab_utils.hpp | 461 +++++++++++++++++++++++------------------
 1 file changed, 257 insertions(+), 204 deletions(-)

diff --git a/src/smithlab_utils.hpp b/src/smithlab_utils.hpp
index e3e9d15..b6d86ea 100644
--- a/src/smithlab_utils.hpp
+++ b/src/smithlab_utils.hpp
@@ -24,201 +24,263 @@
 #ifndef SMITHLAB_UTILS_HPP
 #define SMITHLAB_UTILS_HPP
 
-#include <string>
-#include <sstream>
 #include <algorithm>
-#include <vector>
-#include <iostream>
-#include <ostream>
-#include <limits>
-#include <iterator>
 #include <cassert>
 #include <cmath>
-#include <numeric>
 #include <iomanip>
+#include <iostream>
+#include <iterator>
+#include <limits>
+#include <numeric>
+#include <ostream>
+#include <sstream>
+#include <string>
+#include <vector>
 
-extern "C" {char have_smithlab_cpp();}
-
-namespace smithlab {
-  template <class In, class Out, class Pred> Out
-  copy_if(In first, In last, Out res, Pred p) {
-    while (first != last) {
-      if (p(*first)) *res++ = *first;
-      ++first;
-    }
-    return res;
-  }
-};
+extern "C" {
+char
+have_smithlab_cpp();
+}
 
-typedef size_t MASK_t;
+using MASK_t = std::size_t;
 
 namespace smithlab {
 
-  // Code dealing with false discovery rate
-  double get_fdr_cutoff(const size_t n_tests, std::vector<double> &pvals,
-                        const double alpha);
+// Code dealing with false discovery rate
+double
+get_fdr_cutoff(const std::size_t n_tests, std::vector<double> &pvals,
+               const double alpha);
 
-  void correct_pvals(const size_t n_tests, std::vector<double> &pvals);
+void
+correct_pvals(const std::size_t n_tests, std::vector<double> &pvals);
 
-  // Assumes 4 nucleotide DNA alphabet
-  static const size_t alphabet_size = 4;
+// Assumes 4 nucleotide DNA alphabet
+static const std::size_t alphabet_size = 4;
 
-  std::vector<std::string> split(std::string, const char *,
-                                 bool get_empty_fields = false);
-  std::vector<std::string> split_whitespace_quoted(std::string to_split);
-  void split_whitespace(const std::string& s, std::vector<std::string> &v);
+std::vector<std::string>
+split(std::string, const char *, bool get_empty_fields = false);
+std::vector<std::string>
+split_whitespace_quoted(std::string to_split);
+void
+split_whitespace(const std::string &s, std::vector<std::string> &v);
 
-  std::string strip(const std::string& s);
+std::string
+strip(const std::string &s);
 
-  std::vector<std::string>
-  squash(const std::vector<std::string> &v);
+std::vector<std::string>
+squash(const std::vector<std::string> &v);
 
-  template <class T> std::string toa(T t) {
-    std::ostringstream s;
-    s << t;
-    return s.str();
-  }
-  double log_sum_log_vec(const std::vector<double> &vals, size_t lim);
+template <class T>
+std::string
+toa(T t) {
+  std::ostringstream s;
+  s << t;
+  return s.str();
 }
+double
+log_sum_log_vec(const std::vector<double> &vals, std::size_t lim);
+}  // namespace smithlab
 
 namespace smithlab_bits {
-  static const MASK_t low_bit = 1ul;
-  static const MASK_t high_bit = static_cast<size_t>(0x8000000000000000ul);
-  static const MASK_t all_ones = static_cast<size_t>(-1);
-  static const MASK_t all_zeros = 0ul;
-  static const size_t word_size = 64ul;
-}
-
-inline size_t
+static const MASK_t low_bit = 1ul;
+static const MASK_t high_bit = static_cast<std::size_t>(0x8000000000000000ul);
+static const MASK_t all_ones = static_cast<std::size_t>(-1);
+static const MASK_t all_zeros = 0ul;
+static const std::size_t word_size = 64ul;
+}  // namespace smithlab_bits
+
+inline std::size_t
 base2int_upper_only(char c) {
-  switch(c) {
-  case 'A' : return 0;
-  case 'C' : return 1;
-  case 'G' : return 2;
-  case 'T' : return 3;
-  default  : return 4;
+  switch (c) {
+  case 'A':
+    return 0;
+  case 'C':
+    return 1;
+  case 'G':
+    return 2;
+  case 'T':
+    return 3;
+  default:
+    return 4;
   }
 }
 
-inline size_t
+inline std::size_t
 base2int(char c) {
-  switch(c) {
-  case 'A' : return 0;
-  case 'C' : return 1;
-  case 'G' : return 2;
-  case 'T' : return 3;
-  case 'a' : return 0;
-  case 'c' : return 1;
-  case 'g' : return 2;
-  case 't' : return 3;
-  default  : return 4;
+  switch (c) {
+  case 'A':
+    return 0;
+  case 'C':
+    return 1;
+  case 'G':
+    return 2;
+  case 'T':
+    return 3;
+  case 'a':
+    return 0;
+  case 'c':
+    return 1;
+  case 'g':
+    return 2;
+  case 't':
+    return 3;
+  default:
+    return 4;
   }
 }
 
-inline size_t
+inline std::size_t
 base2int_bs_upper_only(char c) {
-  switch(c) {
-  case 'A' : return 0;
-  case 'C' : return 3;
-  case 'G' : return 2;
-  case 'T' : return 3;
-  default  : return 4;
+  switch (c) {
+  case 'A':
+    return 0;
+  case 'C':
+    return 3;
+  case 'G':
+    return 2;
+  case 'T':
+    return 3;
+  default:
+    return 4;
   }
 }
 
-inline size_t
+inline std::size_t
 base2int_bs(char c) {
-  switch(c) {
-  case 'A' : return 0;
-  case 'C' : return 3;
-  case 'G' : return 2;
-  case 'T' : return 3;
-  case 'a' : return 0;
-  case 'c' : return 3;
-  case 'g' : return 2;
-  case 't' : return 3;
-  default  : return 4;
+  switch (c) {
+  case 'A':
+    return 0;
+  case 'C':
+    return 3;
+  case 'G':
+    return 2;
+  case 'T':
+    return 3;
+  case 'a':
+    return 0;
+  case 'c':
+    return 3;
+  case 'g':
+    return 2;
+  case 't':
+    return 3;
+  default:
+    return 4;
   }
 }
 
-
-inline size_t
+inline std::size_t
 base2int_bs_ag_upper_only(char c) {
-  switch(c) {
-  case 'A' : return 0;
-  case 'C' : return 1;
-  case 'G' : return 0;
-  case 'T' : return 3;
-  default  : return 4;
+  switch (c) {
+  case 'A':
+    return 0;
+  case 'C':
+    return 1;
+  case 'G':
+    return 0;
+  case 'T':
+    return 3;
+  default:
+    return 4;
   }
 }
 
-
-
-inline size_t
+inline std::size_t
 base2int_bs_ag(char c) {
-  switch(c) {
-  case 'A' : return 0;
-  case 'C' : return 1;
-  case 'G' : return 0;
-  case 'T' : return 3;
-  case 'a' : return 0;
-  case 'c' : return 1;
-  case 'g' : return 0;
-  case 't' : return 3;
-  default  : return 4;
+  switch (c) {
+  case 'A':
+    return 0;
+  case 'C':
+    return 1;
+  case 'G':
+    return 0;
+  case 'T':
+    return 3;
+  case 'a':
+    return 0;
+  case 'c':
+    return 1;
+  case 'g':
+    return 0;
+  case 't':
+    return 3;
+  default:
+    return 4;
   }
 }
 
-
-inline size_t
+inline std::size_t
 base2int_bs_rc(char c) {
-  switch(c) {
-  case 'A' : return 0;
-  case 'C' : return 1;
-  case 'G' : return 0;
-  case 'T' : return 3;
-  case 'a' : return 0;
-  case 'c' : return 1;
-  case 'g' : return 0;
-  case 't' : return 3;
+  switch (c) {
+  case 'A':
+    return 0;
+  case 'C':
+    return 1;
+  case 'G':
+    return 0;
+  case 'T':
+    return 3;
+  case 'a':
+    return 0;
+  case 'c':
+    return 1;
+  case 'g':
+    return 0;
+  case 't':
+    return 3;
   }
   return 4;
 }
 
-inline size_t
+inline std::size_t
 base2int_rc(char c) {
-  switch(c) {
-  case 'A' : return 3;
-  case 'C' : return 2;
-  case 'G' : return 1;
-  case 'T' : return 0;
-  case 'a' : return 3;
-  case 'c' : return 2;
-  case 'g' : return 1;
-  case 't' : return 0;
+  switch (c) {
+  case 'A':
+    return 3;
+  case 'C':
+    return 2;
+  case 'G':
+    return 1;
+  case 'T':
+    return 0;
+  case 'a':
+    return 3;
+  case 'c':
+    return 2;
+  case 'g':
+    return 1;
+  case 't':
+    return 0;
   }
   return 4;
 }
 
 inline char
-int2base(size_t c) {
-  switch(c) {
-  case 0 : return 'A';
-  case 1 : return 'C';
-  case 2 : return 'G';
-  case 3 : return 'T';
+int2base(std::size_t c) {
+  switch (c) {
+  case 0:
+    return 'A';
+  case 1:
+    return 'C';
+  case 2:
+    return 'G';
+  case 3:
+    return 'T';
   }
   return 'N';
 }
 
 inline char
-int2base_rc(size_t c) {
-  switch(c) {
-  case 3 : return 'A';
-  case 2 : return 'C';
-  case 1 : return 'G';
-  case 0 : return 'T';
+int2base_rc(std::size_t c) {
+  switch (c) {
+  case 3:
+    return 'A';
+  case 2:
+    return 'C';
+  case 1:
+    return 'G';
+  case 0:
+    return 'T';
   }
   return 'N';
 }
@@ -229,7 +291,7 @@ isvalid(char c) {
 }
 
 inline std::string
-i2mer(size_t n, size_t index) {
+i2mer(std::size_t n, std::size_t index) {
   std::string s(n, ' ');
   do {
     --n;
@@ -240,7 +302,7 @@ i2mer(size_t n, size_t index) {
 }
 
 inline std::string
-i2mer_rc(size_t n, size_t index) {
+i2mer_rc(std::size_t n, std::size_t index) {
   std::string s(n, ' ');
   do {
     --n;
@@ -250,22 +312,22 @@ i2mer_rc(size_t n, size_t index) {
   return s;
 }
 
-inline size_t
+inline std::size_t
 mer2i(const std::string::const_iterator a, std::string::const_iterator b) {
-  size_t multiplier = 1, index = 0;
+  std::size_t multiplier = 1, index = 0;
   do {
     --b;
-    index += base2int(*b)*multiplier;
+    index += base2int(*b) * multiplier;
     multiplier *= smithlab::alphabet_size;
   } while (b > a);
   return index;
 }
 
-inline size_t
+inline std::size_t
 mer2i_rc(std::string::const_iterator a, const std::string::const_iterator b) {
-  size_t multiplier = 1, index = 0;
+  std::size_t multiplier = 1, index = 0;
   do {
-    index += base2int_rc(*a)*multiplier;
+    index += base2int_rc(*a) * multiplier;
     multiplier *= smithlab::alphabet_size;
   } while (++a < b);
   return index;
@@ -276,14 +338,14 @@ struct SMITHLABException : public std::runtime_error {
   std::string message;
 };
 
-
-template <class T> std::string toa(T t) {
+template <class T>
+std::string
+toa(T t) {
   std::ostringstream s;
   s << t;
   return s.str();
 }
 
-
 ////////////////////////////////////////////////////////////////////////
 // Code for dealing with the DNA alphabet
 
@@ -291,7 +353,7 @@ char
 complement(int i);
 
 inline std::string
-revcomp(const std::string& s) {
+revcomp(const std::string &s) {
   std::string r;
   std::transform(s.begin(), s.end(), back_inserter(r), complement);
   std::reverse(r.begin(), r.end());
@@ -299,7 +361,7 @@ revcomp(const std::string& s) {
 }
 
 inline void
-revcomp_inplace(std::string& s) {
+revcomp_inplace(std::string &s) {
   std::transform(s.begin(), s.end(), s.begin(), complement);
   std::reverse(s.begin(), s.end());
 }
@@ -311,92 +373,83 @@ revcomp_inplace(std::string::iterator first, std::string::iterator last) {
 }
 
 inline std::string
-bits2string_masked(size_t mask, size_t bits) {
+bits2string_masked(std::size_t mask, std::size_t bits) {
   std::string s;
-  size_t selector = smithlab_bits::high_bit;
-  for (size_t i = 0; i < smithlab_bits::word_size; ++i) {
+  std::size_t selector = smithlab_bits::high_bit;
+  for (std::size_t i = 0; i < smithlab_bits::word_size; ++i) {
     s += (selector & bits & mask) ? '1' : '0';
     selector >>= 1;
   }
   return s;
 }
 
-
-
 inline std::string
-bits2string_for_positions(size_t positions, size_t bits) {
+bits2string_for_positions(std::size_t positions, std::size_t bits) {
   std::string s;
-  size_t selector = smithlab_bits::high_bit;
-  for (size_t i = 0; i < smithlab_bits::word_size; ++i) {
+  std::size_t selector = smithlab_bits::high_bit;
+  for (std::size_t i = 0; i < smithlab_bits::word_size; ++i) {
     s += (selector & bits) ? '1' : '0';
     selector >>= 1;
   }
-  return s.substr(s.length() - positions);
+  return s.substr(std::size(s) - positions);
 }
 
-inline size_t
-percent(const size_t a, const size_t b) {
-  return static_cast<size_t>((100.0*a)/b);
+inline std::size_t
+percent(const std::size_t a, const std::size_t b) {
+  return static_cast<std::size_t>((100.0 * a) / b);
 }
 
-
-
-
-
 ////////////////////Code from Alphabet//////////////////////
 
-
-
-bool
-inline valid_base(char c) {
+inline bool
+valid_base(char c) {
   char i = std::toupper(c);
   return (i == 'A' || i == 'C' || i == 'G' || i == 'T');
 }
 
-size_t
-inline mer2index(const char *s, size_t n) {
-  size_t multiplier = 1, index = 0;
+inline std::size_t
+mer2index(const char *s, std::size_t n) {
+  std::size_t multiplier = 1, index = 0;
   do {
     --n;
-    index += base2int(s[n])*multiplier;
+    index += base2int(s[n]) * multiplier;
     multiplier *= smithlab::alphabet_size;
   } while (n > 0);
   return index;
 }
 
-size_t
-inline kmer_counts(const std::vector<std::string> &seqs,
-                   std::vector<size_t> &counts, size_t k) {
+inline std::size_t
+kmer_counts(const std::vector<std::string> &seqs,
+            std::vector<std::size_t> &counts, const std::size_t k) {
   counts.clear();
-  size_t nwords =
-    static_cast<size_t>(pow(static_cast<float>(smithlab::alphabet_size),
-                            static_cast<int>(k)));
+  const std::size_t nwords =
+    std::pow(static_cast<float>(smithlab::alphabet_size), static_cast<int>(k));
   counts.resize(nwords, 0);
-  size_t total = 0;
-  for (size_t i = 0; i < seqs.size(); ++i) {
-    char seq[seqs[i].length() + 1];
-    seq[seqs[i].length()] = '\0';
-    copy(seqs[i].begin(), seqs[i].end(), seq);
-    for (size_t j = 0; j < seqs[i].length() - k + 1; ++j)
-      if (std::count_if(seq + j, seq + j + k, &valid_base) ==
-          static_cast<int>(k)) {
-        counts[mer2index(seq + j, k)]++;
+  std::size_t total{};
+  for (const auto &seq : seqs) {
+    const auto n_kmers = std::size(seq) >= k ? std::size(seq) + 1 - k : 0;
+    auto seq_itr = std::cbegin(seq);
+    const auto seq_lim = seq_itr + n_kmers;
+    while (seq_itr != seq_lim) {
+      if (std::all_of(seq_itr, seq_itr + k, &valid_base)) {
+        ++counts[mer2i(seq_itr, seq_itr + k)];
         ++total;
       }
+      ++seq_itr;
+    }
   }
   return total;
 }
 
-
 /*
  * How to use the ProgressBar:
  *
  * //====================================
- * const size_t lim = v.size();
+ * const std::size_t lim = std::size(v);
  * ProgressBar progress(lim);
  * if (VERBOSE)
  *   progress.report(cerr, 0);
- * for (size_t i = 0; i < lim; ++i) {
+ * for (std::size_t i = 0; i < lim; ++i) {
  *   if (VERBOSE && progress.time_to_report(i))
  *     progress.report(cerr, i);
  *   v[i] += x;
@@ -406,28 +459,28 @@ inline kmer_counts(const std::vector<std::string> &seqs,
  */
 class ProgressBar {
 public:
-  ProgressBar(const size_t x, const std::string message = "completion") :
+  ProgressBar(const std::size_t x, const std::string message = "completion") :
     total(x), prev(0), mid_tag(message) {
-    bar_width = max_bar_width - message.length() - 3 - 5;
+    bar_width = max_bar_width - std::size(message) - 3 - 5;
     bar = std::string(bar_width, ' ');
   }
-  bool time_to_report(const size_t i) const {
-    return (static_cast<size_t>((100.0*i)/total) > prev);
+  bool
+  time_to_report(const std::size_t i) const {
+    return (static_cast<std::size_t>((100.0 * i) / total) > prev);
   }
   void
-  report(std::ostream &out, const size_t i);
+  report(std::ostream &out, const std::size_t i);
 
 private:
-
-  size_t total;
-  size_t prev;
-  size_t bar_width;
-  std::string left_tag = "\r[";
+  std::size_t total{};
+  std::size_t prev{};
+  std::size_t bar_width{};
+  std::string left_tag = R"(\r[)";
   std::string mid_tag;
   std::string bar;
-  std::string right_tag = "\%]";
+  std::string right_tag = R"(\%])";
 
-  static const size_t max_bar_width = 72;
+  static constexpr auto max_bar_width{72ul};
 };
 
 #endif