diff --git a/.clang-tidy b/.clang-tidy
new file mode 100644
index 0000000..f5815af
--- /dev/null
+++ b/.clang-tidy
@@ -0,0 +1,5 @@
+---
+Checks: '-*'
+WarningsAsErrors: ''
+HeaderFilterRegex: '.*'
+FormatStyle: none
diff --git a/.cppcheck_suppress b/.cppcheck_suppress
new file mode 100644
index 0000000..5fb7697
--- /dev/null
+++ b/.cppcheck_suppress
@@ -0,0 +1,5 @@
+unmatchedSuppression
+checkersReport
+# Exclude all for now
+*:*.hpp
+*:*.cpp
diff --git a/CMakeLists.txt b/CMakeLists.txt
index fe1ed71..5b4000a 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -32,6 +32,18 @@ set(CMAKE_EXPORT_COMPILE_COMMANDS on)
 
 include(GNUInstallDirs)
 
+if(STATIC_ANALYSIS)
+  include(cmake/static_analysis.cmake)
+endif()
+
+add_compile_options(
+  -Wall
+  -Wextra
+  -Wpedantic
+  -Werror
+  -Wfatal-errors
+)
+
 file(GLOB cpp_files "*.cpp")
 
 set(LIBRARY_OBJECTS "")
@@ -42,5 +54,9 @@ foreach(cpp_file ${cpp_files})
 endforeach()
 
 add_library(smithlab_cpp)
-target_include_directories(smithlab_cpp PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
-target_link_libraries(smithlab_cpp PUBLIC ${LIBRARY_OBJECTS})
+target_include_directories(smithlab_cpp PUBLIC
+  ${CMAKE_CURRENT_SOURCE_DIR}
+)
+target_link_libraries(smithlab_cpp PUBLIC
+  ${LIBRARY_OBJECTS}
+)
diff --git a/CPPLINT.cfg b/CPPLINT.cfg
new file mode 100644
index 0000000..9e33754
--- /dev/null
+++ b/CPPLINT.cfg
@@ -0,0 +1 @@
+exclude_files=.*\.*pp
diff --git a/GenomicRegion.cpp b/GenomicRegion.cpp
index 8922142..8874fb5 100644
--- a/GenomicRegion.cpp
+++ b/GenomicRegion.cpp
@@ -21,11 +21,15 @@
  */
 
 #include "GenomicRegion.hpp"
-
-#include <exception>
+#include "smithlab_os.hpp"
 
 #include <cassert>
+#include <cctype>
+#include <cstdlib>
 #include <fstream>
+#include <limits>
+#include <sstream>
+#include <stdexcept>
 #include <unordered_map>
 
 using std::ostringstream;
@@ -136,8 +140,6 @@ bool SimpleGenomicRegion::operator!=(const SimpleGenomicRegion &rhs) const {
   return (chrom != rhs.chrom || start != rhs.start || end != rhs.end);
 }
 
-#include <iostream>
-
 unordered_map<string, chrom_id_type> GenomicRegion::fw_table_in;
 unordered_map<chrom_id_type, string> GenomicRegion::fw_table_out;
 
diff --git a/GenomicRegion.hpp b/GenomicRegion.hpp
index f138cf3..08ab8d9 100644
--- a/GenomicRegion.hpp
+++ b/GenomicRegion.hpp
@@ -24,19 +24,20 @@
 #ifndef GENOMIC_REGION_HPP
 #define GENOMIC_REGION_HPP
 
-#include "smithlab_os.hpp"
 #include "smithlab_utils.hpp"
 
+#include <algorithm>
 #include <fstream>
-#include <limits>
+#include <iterator>
+#include <stdio.h>
 #include <string>
 #include <unordered_map>
+#include <utility>
 #include <vector>
+class GenomicRegion;
 
 typedef unsigned chrom_id_type;
 
-class GenomicRegion;
-
 class SimpleGenomicRegion {
 public:
   SimpleGenomicRegion() : chrom(assign_chrom("(null)")), start(0), end(0) {}
diff --git a/MappedRead.cpp b/MappedRead.cpp
index a242486..52074c2 100644
--- a/MappedRead.cpp
+++ b/MappedRead.cpp
@@ -21,11 +21,11 @@
  */
 
 #include "MappedRead.hpp"
-#include "smithlab_utils.hpp"
 
 #include <algorithm>
-#include <fstream>
+#include <cctype>
 #include <sstream>
+#include <stdexcept>
 #include <string>
 
 using std::runtime_error;
diff --git a/MappedRead.hpp b/MappedRead.hpp
index e624418..35bc880 100644
--- a/MappedRead.hpp
+++ b/MappedRead.hpp
@@ -24,6 +24,8 @@
 #define MAPPED_READ_HPP
 
 #include "GenomicRegion.hpp"
+#include <cstdio>
+#include <string>
 
 struct MappedRead {
   MappedRead() {}
diff --git a/OptionParser.cpp b/OptionParser.cpp
index 8bc5fb4..29e29a9 100644
--- a/OptionParser.cpp
+++ b/OptionParser.cpp
@@ -22,20 +22,18 @@
  */
 
 #include "OptionParser.hpp"
+#include "smithlab_utils.hpp"
 
+#include <algorithm>
 #include <cassert>
 #include <cctype>
 #include <cstdlib>
-#include <cstring>
-#include <exception>
 #include <fstream>
-#include <functional>
 #include <iomanip>
 #include <iterator>
 #include <regex>
 #include <sstream>
-
-#include "smithlab_utils.hpp"
+#include <stdexcept>
 
 using std::begin;
 using std::end;
diff --git a/OptionParser.hpp b/OptionParser.hpp
index 60484f5..ec51756 100644
--- a/OptionParser.hpp
+++ b/OptionParser.hpp
@@ -19,6 +19,7 @@
 #ifndef OPTION_PARSER_HPP
 #define OPTION_PARSER_HPP
 
+#include <cstddef>
 #include <limits>
 #include <string>
 #include <vector>
diff --git a/QualityScore.cpp b/QualityScore.cpp
index a236bfb..6e2b0a4 100644
--- a/QualityScore.cpp
+++ b/QualityScore.cpp
@@ -22,8 +22,9 @@
 
 #include "QualityScore.hpp"
 
-#include "smithlab_utils.hpp"
+#include <cctype>
 #include <fstream>
+#include <stdexcept>
 
 using std::runtime_error;
 using std::string;
diff --git a/QualityScore.hpp b/QualityScore.hpp
index 1cf1010..9b49ce2 100644
--- a/QualityScore.hpp
+++ b/QualityScore.hpp
@@ -25,6 +25,7 @@
 
 #include <algorithm>
 #include <cmath>
+#include <cstddef>
 #include <string>
 
 ////////////////////////////////////////////////////////////////////////
diff --git a/bisulfite_utils.cpp b/bisulfite_utils.cpp
index b43d9b4..9ddb034 100644
--- a/bisulfite_utils.cpp
+++ b/bisulfite_utils.cpp
@@ -22,14 +22,12 @@
  */
 
 #include "bisulfite_utils.hpp"
+#include <cctype>
 #include <cstdlib>
-#include <iostream>
 #include <random>
 
-using std::string;
-
-void bisulfite_treatment(std::mt19937 &generator, string &seq, double bs_rate,
-                         double meth_rate) {
+void bisulfite_treatment(std::mt19937 &generator, std::string &seq,
+                         double bs_rate, double meth_rate) {
 
   std::uniform_real_distribution<double> unif(0.0, 1.0);
 
diff --git a/chromosome_utils.cpp b/chromosome_utils.cpp
index e4d82f4..e97b599 100644
--- a/chromosome_utils.cpp
+++ b/chromosome_utils.cpp
@@ -21,8 +21,16 @@
  */
 
 #include "chromosome_utils.hpp"
+#include "GenomicRegion.hpp"
+#include "smithlab_os.hpp"
 
+#include <algorithm>
+#include <cassert>
 #include <cctype>
+#include <cmath>
+#include <cstdlib>
+#include <fstream>
+#include <iterator>
 #include <stdexcept>
 #include <string>
 #include <unordered_map>
diff --git a/chromosome_utils.hpp b/chromosome_utils.hpp
index 0e79c90..9d77cb1 100644
--- a/chromosome_utils.hpp
+++ b/chromosome_utils.hpp
@@ -23,18 +23,13 @@
 #ifndef CHROMOSOME_UTILS_HPP
 #define CHROMOSOME_UTILS_HPP
 
-#include <algorithm>
-#include <cassert>
-#include <cmath>
-#include <iostream>
-#include <iterator>
-#include <limits>
-#include <ostream>
-#include <sstream>
+#include <cstddef>
 #include <string>
+#include <unordered_map>
 #include <vector>
 
-#include "GenomicRegion.hpp"
+class GenomicRegion;
+class SimpleGenomicRegion;
 
 void parse_region_name(std::string region_name, std::string &chrom,
                        size_t &start, size_t &end);
diff --git a/cigar_utils.cpp b/cigar_utils.cpp
index 43e6d73..232342e 100644
--- a/cigar_utils.cpp
+++ b/cigar_utils.cpp
@@ -15,8 +15,8 @@
 
 #include "cigar_utils.hpp"
 
-#include <exception>
 #include <sstream>
+#include <stdexcept>
 #include <string>
 
 using std::runtime_error;
diff --git a/cigar_utils.hpp b/cigar_utils.hpp
index e1e8eea..a96539e 100644
--- a/cigar_utils.hpp
+++ b/cigar_utils.hpp
@@ -17,7 +17,10 @@
 #define CIGAR_UTILS_HPP
 
 #include <algorithm>
-#include <cctype> // isdigit
+#include <cctype>
+#include <cstdio>
+#include <initializer_list>
+#include <iterator>
 #include <string>
 
 inline bool consumes_query(const char op) {
diff --git a/cmake/static_analysis.cmake b/cmake/static_analysis.cmake
new file mode 100644
index 0000000..f1323ad
--- /dev/null
+++ b/cmake/static_analysis.cmake
@@ -0,0 +1,119 @@
+# Copyright (C) 2025 Andrew D Smith
+#
+# This program 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.
+#
+# This program 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.
+#
+# You should have received a copy of the GNU General Public License along with
+# this program. If not, see <https://www.gnu.org/licenses/>.
+
+# StaticAnalysis
+message(STATUS "Enabling static analysis")
+# If no specific static analysis is requested, do them all
+if(NOT RUN_CPPCHECK AND NOT RUN_IWYU AND
+    NOT RUN_CPPLINT  AND NOT RUN_CLANG_TIDY)
+  set(RUN_CPPCHECK on)
+  set(RUN_IWYU on)
+  set(RUN_CPPLINT on)
+  set(RUN_CLANG_TIDY on)
+endif()
+
+set(STATIC_ANALYSIS_CHECKS "")
+if(RUN_CPPCHECK)
+  list(APPEND STATIC_ANALYSIS_CHECKS "cppcheck")
+endif()
+if(RUN_CPPLINT)
+  list(APPEND STATIC_ANALYSIS_CHECKS "cpplint")
+endif()
+if(RUN_IWYU)
+  list(APPEND STATIC_ANALYSIS_CHECKS "iwyu")
+endif()
+if(RUN_CLANG_TIDY)
+  list(APPEND STATIC_ANALYSIS_CHECKS "clang-tidy")
+endif()
+
+message(STATUS "Requested static analysis: ${STATIC_ANALYSIS_CHECKS}")
+
+# cpplint: all options are in the config file
+if ("cpplint" IN_LIST STATIC_ANALYSIS_CHECKS)
+  find_program(FOUND_CPPLINT cpplint)
+  if(FOUND_CPPLINT)
+    message(STATUS "Enabling cpplint analysis")
+    set(CMAKE_CXX_CPPLINT cpplint --quiet)
+  else()
+    message(STATUS "Could not find cpplint; disabling cpplint")
+  endif()
+endif()
+
+# include-what-you-use: config is a mappings file
+if ("iwyu" IN_LIST STATIC_ANALYSIS_CHECKS)
+  find_program(FOUND_IWYU include-what-you-use)
+  if(FOUND_IWYU)
+    message(STATUS "Enabling include-what-you-use analysis")
+    set(CMAKE_CXX_INCLUDE_WHAT_YOU_USE
+      include-what-you-use
+      -Xiwyu
+      --comment_style=none
+      -Xiwyu
+      --quoted_includes_first
+      -Xiwyu
+      --mapping_file=${PROJECT_SOURCE_DIR}/iwyu.json
+    )
+  else()
+    message(STATUS "Could not find iwyu; disabling iwyu")
+  endif()
+endif()
+
+# cppcheck: options on the command line as there is no config file
+if ("cppcheck" IN_LIST STATIC_ANALYSIS_CHECKS)
+  find_program(FOUND_CPPCHECK cppcheck)
+  if(FOUND_CPPCHECK)
+    message(STATUS "Enabling cppcheck analysis")
+    set(CMAKE_CXX_CPPCHECK
+      cppcheck
+      --quiet
+      --enable=all
+      --inline-suppr
+      --max-configs=1
+      --suppressions-list=${PROJECT_SOURCE_DIR}/.cppcheck_suppress
+    )
+  else()
+    message(STATUS "Could not find cppcheck; disabling cppcheck")
+  endif()
+endif()
+
+# clang-tidy: need to make sure version is at least 20
+if ("clang-tidy" IN_LIST STATIC_ANALYSIS_CHECKS)
+  find_program(CLANG_TIDY_EXECUTABLE NAMES clang-tidy)
+  # Minimum required version
+  set(MIN_CLANG_TIDY_VERSION "20.0.0")
+  if(CLANG_TIDY_EXECUTABLE)
+    execute_process(
+      COMMAND
+      bash -c
+      "${CLANG_TIDY_EXECUTABLE} --version | grep version | tr -cd '0-9.\n'"
+      OUTPUT_VARIABLE CLANG_TIDY_VERSION
+      OUTPUT_STRIP_TRAILING_WHITESPACE
+    )
+    # Compare the version numbers
+    if(CLANG_TIDY_VERSION VERSION_GREATER_EQUAL MIN_CLANG_TIDY_VERSION)
+      message(STATUS "Enabling clang-tidy (version: ${CLANG_TIDY_VERSION})")
+      set(CMAKE_CXX_CLANG_TIDY
+        clang-tidy
+        --quiet
+        --allow-no-checks
+        -p ${PROJECT_BINARY_DIR}
+      )
+    else()
+      message(STATUS "Not enabling clang-tidy (min version not found")
+    endif()
+  else()
+    message(STATUS "Could not find clang-tidy; disabling clang-tidy")
+  endif()
+endif()
diff --git a/dna_four_bit.hpp b/dna_four_bit.hpp
index 9724dda..c54d3d1 100644
--- a/dna_four_bit.hpp
+++ b/dna_four_bit.hpp
@@ -17,8 +17,10 @@
 #ifndef DNA_FOUR_BIT_HPP
 #define DNA_FOUR_BIT_HPP
 
+#include <cstddef>
 #include <cstdint>
-#include <iterator>
+#include <iterator> // IWYU pragma: keep
+#include <utility>
 #include <vector>
 
 enum base_in_byte { left, right };
diff --git a/htslib_wrapper.cpp b/htslib_wrapper.cpp
index 938a1f3..c7a9e44 100644
--- a/htslib_wrapper.cpp
+++ b/htslib_wrapper.cpp
@@ -17,15 +17,14 @@
  */
 
 #include "htslib_wrapper.hpp"
+#include "sam_record.hpp"
 
-#include <fstream>
+#include <cassert>
 #include <iostream>
+#include <stdexcept>
 #include <string>
 #include <vector>
 
-#include "MappedRead.hpp"
-#include "smithlab_utils.hpp"
-
 using std::cerr;
 using std::endl;
 using std::runtime_error;
diff --git a/htslib_wrapper.hpp b/htslib_wrapper.hpp
index 51c268c..0a23243 100644
--- a/htslib_wrapper.hpp
+++ b/htslib_wrapper.hpp
@@ -18,17 +18,13 @@
 #ifndef HTSLIB_WRAPPER_HPP
 #define HTSLIB_WRAPPER_HPP
 
-#include <fstream>
-#include <string>
-#include <vector>
-
-#include "sam_record.hpp"
-#include "smithlab_utils.hpp"
-
-extern "C" {
 #include <htslib/hts.h>
 #include <htslib/sam.h>
-}
+
+#include <cstddef>
+#include <string>
+
+class sam_rec;
 
 extern "C" {
 char check_htslib_wrapper();
diff --git a/iwyu.json b/iwyu.json
new file mode 100644
index 0000000..0d4f101
--- /dev/null
+++ b/iwyu.json
@@ -0,0 +1,2 @@
+[
+]
diff --git a/sam_record.cpp b/sam_record.cpp
index 2b04839..9af0120 100644
--- a/sam_record.cpp
+++ b/sam_record.cpp
@@ -17,13 +17,12 @@
  */
 
 #include "sam_record.hpp"
+#include "cigar_utils.hpp"
 
 #include <cstdint>
 #include <regex>
 #include <sstream>
-
-#include "cigar_utils.hpp"
-#include "smithlab_utils.hpp"
+#include <stdexcept>
 
 using std::begin;
 using std::end;
diff --git a/sam_record.hpp b/sam_record.hpp
index 7b837b4..5dcaefa 100644
--- a/sam_record.hpp
+++ b/sam_record.hpp
@@ -19,8 +19,9 @@
 #ifndef SAM_RECORD_HPP
 #define SAM_RECORD_HPP
 
+#include <algorithm>
+#include <cstddef>
 #include <cstdint>
-#include <iostream>
 #include <iterator>
 #include <sstream>
 #include <string>
diff --git a/smithlab_os.cpp b/smithlab_os.cpp
index 8e33d46..b008870 100644
--- a/smithlab_os.cpp
+++ b/smithlab_os.cpp
@@ -16,22 +16,21 @@
  * General Public License for more details.
  */
 
+#include "smithlab_os.hpp"
+#include "QualityScore.hpp"
+#include "smithlab_utils.hpp"
+
 #include <algorithm>
-#include <cmath>
+#include <cassert>
+#include <cerrno>
 #include <cstring>
-#include <exception>
 #include <filesystem>
 #include <fstream>
-#include <iostream>
-#include <map>
+#include <iterator>
+#include <stdexcept>
 #include <unordered_map>
 
-#include "QualityScore.hpp"
-#include "smithlab_os.hpp"
-#include "smithlab_utils.hpp"
-
 #include <dirent.h>
-#include <errno.h>
 #include <sys/stat.h>
 #include <unistd.h>
 
diff --git a/smithlab_os.hpp b/smithlab_os.hpp
index c647d70..d1d4d33 100644
--- a/smithlab_os.hpp
+++ b/smithlab_os.hpp
@@ -19,6 +19,7 @@
 #ifndef SMITHLAB_OS_HPP
 #define SMITHLAB_OS_HPP
 
+#include <cstddef>
 #include <string>
 #include <unordered_map>
 #include <vector>
diff --git a/smithlab_utils.cpp b/smithlab_utils.cpp
index c21f71e..1e52a29 100644
--- a/smithlab_utils.cpp
+++ b/smithlab_utils.cpp
@@ -21,9 +21,14 @@
  */
 
 #include "smithlab_utils.hpp"
+
+#include <cassert>
 #include <cmath>
 #include <cstring>
+#include <iomanip>
+#include <limits>
 #include <string>
+#include <utility>
 
 using std::string;
 using std::vector;
diff --git a/smithlab_utils.hpp b/smithlab_utils.hpp
index e4cd338..ff46771 100644
--- a/smithlab_utils.hpp
+++ b/smithlab_utils.hpp
@@ -25,15 +25,10 @@
 #define SMITHLAB_UTILS_HPP
 
 #include <algorithm>
-#include <cassert>
+#include <cctype>
 #include <cmath>
-#include <cstdint>
-#include <iomanip>
-#include <iostream>
+#include <cstddef>
 #include <iterator>
-#include <limits>
-#include <numeric>
-#include <ostream>
 #include <sstream>
 #include <string>
 #include <vector>
diff --git a/zlib_wrapper.cpp b/zlib_wrapper.cpp
index 7957f2d..2d5aafd 100644
--- a/zlib_wrapper.cpp
+++ b/zlib_wrapper.cpp
@@ -16,8 +16,7 @@
 #include "zlib_wrapper.hpp"
 
 #include <algorithm>
-
-using std::string;
+#include <iterator>
 
 char igzfstream::peek() {
   const char c = gzgetc(fileobj);
@@ -26,7 +25,7 @@ char igzfstream::peek() {
   return c;
 }
 
-igzfstream &getline(igzfstream &in, string &line) {
+igzfstream &getline(igzfstream &in, std::string &line) {
   if (gzgets(in.fileobj, &in.buf[0], in.chunk_size)) {
     auto eol = std::find(begin(in.buf), end(in.buf), '\n');
     line.clear();
@@ -36,11 +35,11 @@ igzfstream &getline(igzfstream &in, string &line) {
   return in;
 }
 
-igzfstream &operator>>(igzfstream &in, string &line) {
+igzfstream &operator>>(igzfstream &in, std::string &line) {
   return getline(in, line);
 }
 
-ogzfstream &operator<<(ogzfstream &out, const string &line) {
+ogzfstream &operator<<(ogzfstream &out, const std::string &line) {
   gzputs(out.fileobj, line.c_str());
   return out;
 }
diff --git a/zlib_wrapper.hpp b/zlib_wrapper.hpp
index bdbf5cd..2823fee 100644
--- a/zlib_wrapper.hpp
+++ b/zlib_wrapper.hpp
@@ -16,12 +16,12 @@
 #ifndef ZLIB_WRAPPER_HPP
 #define ZLIB_WRAPPER_HPP
 
+#include <zlib.h>
+
+#include <cstddef>
 #include <string>
 #include <vector>
 
-// ADS: need some way to check if this is installed
-#include <zlib.h>
-
 struct igzfstream {
   igzfstream(const std::string filename)
       : fileobj(gzopen(filename.c_str(), "r")) {