Threading bugfix for amrfinder

Makefile.am

@@ -147,6 +147,8 @@ test_scripts/test_unxcounts.log: test_scripts/test_xcounts.log
 
 noinst_LIBRARIES = libdnmtools.a
 libdnmtools_a_SOURCES = \
+        src/common/Interval.cpp \
+        src/common/Interval6.cpp \
         src/common/dnmtools_gaussinv.cpp \
         src/common/bam_record_utils.cpp \
         src/common/counts_header.cpp \
@@ -166,6 +168,8 @@ libdnmtools_a_SOURCES = \
 	src/common/dnmtools_utils.cpp
 
 libdnmtools_a_SOURCES += \
+        src/common/Interval.hpp \
+        src/common/Interval6.hpp \
 	src/bamxx/bamxx.hpp \
         src/common/dnmtools_gaussinv.hpp \
 	src/common/bam_record_utils.hpp \

configure.ac

@@ -30,7 +30,7 @@ AS_IF([test "x$CXXFLAGS_set" != "xset"], [
 ])
 AC_MSG_NOTICE([CXXFLAGS is $CXXFLAGS])
 
-AX_CXX_COMPILE_STDCXX_17([noext], [mandatory])
+AX_CXX_COMPILE_STDCXX(17, [noext], [mandatory])
 AC_PROG_RANLIB
 
 dnl recursively configure abismal and smithlab_cpp

m4/ax_cxx_compile_stdcxx.m4

@@ -10,13 +10,13 @@
 #
 #   Check for baseline language coverage in the compiler for the specified
 #   version of the C++ standard.  If necessary, add switches to CXX and
-#   CXXCPP to enable support.  VERSION may be '11' (for the C++11 standard)
-#   or '14' (for the C++14 standard).
+#   CXXCPP to enable support.  VERSION may be '11', '14', '17', '20', or
+#   '23' for the respective C++ standard version.
 #
 #   The second argument, if specified, indicates whether you insist on an
 #   extended mode (e.g. -std=gnu++11) or a strict conformance mode (e.g.
 #   -std=c++11).  If neither is specified, you get whatever works, with
-#   preference for an extended mode.
+#   preference for no added switch, and then for an extended mode.
 #
 #   The third argument, if specified 'mandatory' or if left unspecified,
 #   indicates that baseline support for the specified C++ standard is
@@ -35,13 +35,16 @@
 #   Copyright (c) 2015 Moritz Klammler <moritz@klammler.eu>
 #   Copyright (c) 2016, 2018 Krzesimir Nowak <qdlacz@gmail.com>
 #   Copyright (c) 2019 Enji Cooper <yaneurabeya@gmail.com>
+#   Copyright (c) 2020 Jason Merrill <jason@redhat.com>
+#   Copyright (c) 2021, 2024 Jörn Heusipp <osmanx@problemloesungsmaschine.de>
+#   Copyright (c) 2015, 2022, 2023, 2024 Olly Betts
 #
 #   Copying and distribution of this file, with or without modification, are
 #   permitted in any medium without royalty provided the copyright notice
 #   and this notice are preserved.  This file is offered as-is, without any
 #   warranty.
 
-#serial 11
+#serial 25
 
 dnl  This macro is based on the code from the AX_CXX_COMPILE_STDCXX_11 macro
 dnl  (serial version number 13).
@@ -50,6 +53,8 @@ AC_DEFUN([AX_CXX_COMPILE_STDCXX], [dnl
   m4_if([$1], [11], [ax_cxx_compile_alternatives="11 0x"],
         [$1], [14], [ax_cxx_compile_alternatives="14 1y"],
         [$1], [17], [ax_cxx_compile_alternatives="17 1z"],
+        [$1], [20], [ax_cxx_compile_alternatives="20"],
+        [$1], [23], [ax_cxx_compile_alternatives="23"],
         [m4_fatal([invalid first argument `$1' to AX_CXX_COMPILE_STDCXX])])dnl
   m4_if([$2], [], [],
         [$2], [ext], [],
@@ -62,6 +67,16 @@ AC_DEFUN([AX_CXX_COMPILE_STDCXX], [dnl
   AC_LANG_PUSH([C++])dnl
   ac_success=no
 
+  m4_if([$2], [], [dnl
+    AC_CACHE_CHECK(whether $CXX supports C++$1 features by default,
+		   ax_cv_cxx_compile_cxx$1,
+      [AC_COMPILE_IFELSE([AC_LANG_SOURCE([_AX_CXX_COMPILE_STDCXX_testbody_$1])],
+        [ax_cv_cxx_compile_cxx$1=yes],
+        [ax_cv_cxx_compile_cxx$1=no])])
+    if test x$ax_cv_cxx_compile_cxx$1 = xyes; then
+      ac_success=yes
+    fi])
+
   m4_if([$2], [noext], [], [dnl
   if test x$ac_success = xno; then
     for alternative in ${ax_cxx_compile_alternatives}; do
@@ -91,9 +106,18 @@ AC_DEFUN([AX_CXX_COMPILE_STDCXX], [dnl
     dnl HP's aCC needs +std=c++11 according to:
     dnl http://h21007.www2.hp.com/portal/download/files/unprot/aCxx/PDF_Release_Notes/769149-001.pdf
     dnl Cray's crayCC needs "-h std=c++11"
+    dnl MSVC needs -std:c++NN for C++17 and later (default is C++14)
     for alternative in ${ax_cxx_compile_alternatives}; do
-      for switch in -std=c++${alternative} +std=c++${alternative} "-h std=c++${alternative}"; do
-        cachevar=AS_TR_SH([ax_cv_cxx_compile_cxx$1_$switch])
+      for switch in -std=c++${alternative} +std=c++${alternative} "-h std=c++${alternative}" MSVC; do
+        if test x"$switch" = xMSVC; then
+          dnl AS_TR_SH maps both `:` and `=` to `_` so -std:c++17 would collide
+          dnl with -std=c++17.  We suffix the cache variable name with _MSVC to
+          dnl avoid this.
+          switch=-std:c++${alternative}
+          cachevar=AS_TR_SH([ax_cv_cxx_compile_cxx$1_${switch}_MSVC])
+        else
+          cachevar=AS_TR_SH([ax_cv_cxx_compile_cxx$1_$switch])
+        fi
         AC_CACHE_CHECK(whether $CXX supports C++$1 features with $switch,
                        $cachevar,
           [ac_save_CXX="$CXX"
@@ -137,23 +161,44 @@ AC_DEFUN([AX_CXX_COMPILE_STDCXX], [dnl
 dnl  Test body for checking C++11 support
 
 m4_define([_AX_CXX_COMPILE_STDCXX_testbody_11],
-  _AX_CXX_COMPILE_STDCXX_testbody_new_in_11
+  [_AX_CXX_COMPILE_STDCXX_testbody_new_in_11]
 )
 
-
 dnl  Test body for checking C++14 support
 
 m4_define([_AX_CXX_COMPILE_STDCXX_testbody_14],
-  _AX_CXX_COMPILE_STDCXX_testbody_new_in_11
-  _AX_CXX_COMPILE_STDCXX_testbody_new_in_14
+  [_AX_CXX_COMPILE_STDCXX_testbody_new_in_11
+   _AX_CXX_COMPILE_STDCXX_testbody_new_in_14]
 )
 
+dnl  Test body for checking C++17 support
+
 m4_define([_AX_CXX_COMPILE_STDCXX_testbody_17],
-  _AX_CXX_COMPILE_STDCXX_testbody_new_in_11
-  _AX_CXX_COMPILE_STDCXX_testbody_new_in_14
-  _AX_CXX_COMPILE_STDCXX_testbody_new_in_17
+  [_AX_CXX_COMPILE_STDCXX_testbody_new_in_11
+   _AX_CXX_COMPILE_STDCXX_testbody_new_in_14
+   _AX_CXX_COMPILE_STDCXX_testbody_new_in_17]
+)
+
+dnl  Test body for checking C++20 support
+
+m4_define([_AX_CXX_COMPILE_STDCXX_testbody_20],
+  [_AX_CXX_COMPILE_STDCXX_testbody_new_in_11
+   _AX_CXX_COMPILE_STDCXX_testbody_new_in_14
+   _AX_CXX_COMPILE_STDCXX_testbody_new_in_17
+   _AX_CXX_COMPILE_STDCXX_testbody_new_in_20]
 )
 
+dnl  Test body for checking C++23 support
+
+m4_define([_AX_CXX_COMPILE_STDCXX_testbody_23],
+  [_AX_CXX_COMPILE_STDCXX_testbody_new_in_11
+   _AX_CXX_COMPILE_STDCXX_testbody_new_in_14
+   _AX_CXX_COMPILE_STDCXX_testbody_new_in_17
+   _AX_CXX_COMPILE_STDCXX_testbody_new_in_20
+   _AX_CXX_COMPILE_STDCXX_testbody_new_in_23]
+)
+
+
 dnl  Tests for new features in C++11
 
 m4_define([_AX_CXX_COMPILE_STDCXX_testbody_new_in_11], [[
@@ -165,7 +210,21 @@ m4_define([_AX_CXX_COMPILE_STDCXX_testbody_new_in_11], [[
 
 #error "This is not a C++ compiler"
 
-#elif __cplusplus < 201103L
+// MSVC always sets __cplusplus to 199711L in older versions; newer versions
+// only set it correctly if /Zc:__cplusplus is specified as well as a
+// /std:c++NN switch:
+//
+// https://devblogs.microsoft.com/cppblog/msvc-now-correctly-reports-__cplusplus/
+//
+// The value __cplusplus ought to have is available in _MSVC_LANG since
+// Visual Studio 2015 Update 3:
+//
+// https://learn.microsoft.com/en-us/cpp/preprocessor/predefined-macros
+//
+// This was also the first MSVC version to support C++14 so we can't use the
+// value of either __cplusplus or _MSVC_LANG to quickly rule out MSVC having
+// C++11 or C++14 support, but we can check _MSVC_LANG for C++17 and later.
+#elif __cplusplus < 201103L && !defined _MSC_VER
 
 #error "This is not a C++11 compiler"
 
@@ -456,7 +515,7 @@ m4_define([_AX_CXX_COMPILE_STDCXX_testbody_new_in_14], [[
 
 #error "This is not a C++ compiler"
 
-#elif __cplusplus < 201402L
+#elif __cplusplus < 201402L && !defined _MSC_VER
 
 #error "This is not a C++14 compiler"
 
@@ -580,7 +639,7 @@ m4_define([_AX_CXX_COMPILE_STDCXX_testbody_new_in_17], [[
 
 #error "This is not a C++ compiler"
 
-#elif __cplusplus < 201703L
+#elif (defined _MSVC_LANG ? _MSVC_LANG : __cplusplus) < 201703L
 
 #error "This is not a C++17 compiler"
 
@@ -946,6 +1005,66 @@ namespace cxx17
 
 }  // namespace cxx17
 
-#endif  // __cplusplus < 201703L
+#endif  // (defined _MSVC_LANG ? _MSVC_LANG : __cplusplus) < 201703L
+
+]])
+
+
+dnl  Tests for new features in C++20
+
+m4_define([_AX_CXX_COMPILE_STDCXX_testbody_new_in_20], [[
+
+#ifndef __cplusplus
+
+#error "This is not a C++ compiler"
+
+#elif (defined _MSVC_LANG ? _MSVC_LANG : __cplusplus) < 202002L
+
+#error "This is not a C++20 compiler"
+
+#else
+
+#include <version>
+
+namespace cxx20
+{
+
+// As C++20 supports feature test macros in the standard, there is no
+// immediate need to actually test for feature availability on the
+// Autoconf side.
+
+}  // namespace cxx20
+
+#endif  // (defined _MSVC_LANG ? _MSVC_LANG : __cplusplus) < 202002L
+
+]])
+
+
+dnl  Tests for new features in C++23
+
+m4_define([_AX_CXX_COMPILE_STDCXX_testbody_new_in_23], [[
+
+#ifndef __cplusplus
+
+#error "This is not a C++ compiler"
+
+#elif (defined _MSVC_LANG ? _MSVC_LANG : __cplusplus) < 202302L
+
+#error "This is not a C++23 compiler"
+
+#else
+
+#include <version>
+
+namespace cxx23
+{
+
+// As C++23 supports feature test macros in the standard, there is no
+// immediate need to actually test for feature availability on the
+// Autoconf side.
+
+}  // namespace cxx23
+
+#endif  // (defined _MSVC_LANG ? _MSVC_LANG : __cplusplus) < 202302L
 
 ]])