Using mod functions from htslib

.cppcheck_suppress

@@ -1,24 +1,18 @@
-# MIT License
+# This file is part of dnmtools
 #
-# Copyright (c) 2024 Andrew Smith
+# Copyright (C) 2023-2025 Andrew D. Smith
 #
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
+# Authors: Andrew D. Smith
 #
-# The above copyright notice and this permission notice shall be included in all
-# copies or substantial portions of the Software.
+# This 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.
 #
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-# SOFTWARE.
+# This software 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.
 
 missingIncludeSystem
 constVariablePointer

.github/workflows/dnmtools_build_ubuntu.yml

@@ -15,28 +15,56 @@ jobs:
       with:
         submodules: recursive
     - name: Install dependencies
-      run: sudo apt-get install -y libhts-dev libgsl-dev
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y \
+        libgsl-dev \
+        libcurl4-gnutls-dev \
+        libdeflate-dev \
+        liblzma-dev \
+        zlib1g-dev \
+        libbz2-dev
+    - name: Build and install htslib (for recent version)
+      run: |
+        git clone --recursive https://github.com/samtools/htslib.git
+        cd htslib
+        make -j4
+        sudo make install prefix=/usr
     - name: Generate configure script
       run: ./autogen.sh
     - name: Configure for GCC
       run: ./configure CXX="g++"
     - name: Build with g++
       run: make -j4
     - name: Test the g++ build
-      run: make -j4 check-TESTS
+      run: make -j4 check
   build-with-clang:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
       with:
         submodules: recursive
     - name: Install dependencies
-      run: sudo apt-get install -y libhts-dev libgsl-dev
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y \
+        libgsl-dev \
+        libcurl4-gnutls-dev \
+        libdeflate-dev \
+        liblzma-dev \
+        zlib1g-dev \
+        libbz2-dev
+    - name: Build and install htslib (for recent version)
+      run: |
+        git clone --recursive https://github.com/samtools/htslib.git
+        cd htslib
+        make -j4
+        sudo make install prefix=/usr
     - name: Generate configure script
       run: ./autogen.sh
     - name: Configure for Clang
       run: ./configure CXX="clang++"
     - name: Build with clang++
       run: make -j4
     - name: Test the clang++ build
-      run: make -j4 check-TESTS
+      run: make -j4 check

.github/workflows/dnmtools_distcheck_ubuntu.yml

@@ -14,26 +14,27 @@ jobs:
     - uses: actions/checkout@v4
       with:
         submodules: recursive
-    - name: Get version number
-      id: vn
-      run: |
-        awk '/AC_INIT/ {print "vn="$2}' configure.ac | sed "s/\[//; s/\]//; s/,//" >> "$GITHUB_OUTPUT"
-      env:
-        GH_TOKEN: ${{ github.token }}
-    - name: Update packages
-      run: sudo apt-get update
     - name: Install dependencies
-      run: sudo apt-get install -y libhts-dev libgsl-dev samtools
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y \
+        libgsl-dev \
+        libcurl4-gnutls-dev \
+        libdeflate-dev \
+        liblzma-dev \
+        zlib1g-dev \
+        libbz2-dev
+    - name: Build and install htslib (for recent version)
+      run: |
+        git clone --recursive https://github.com/samtools/htslib.git
+        cd htslib
+        make -j4
+        sudo make install prefix=/usr
     - name: Generate configure script
       run: ./autogen.sh
     - name: configure
       run: ./configure
     - name: Generate the source archive
       run: make dist
-    - name: Upload the archive
-      uses: actions/upload-artifact@v4
-      with:
-        name: dnmtools-${{ steps.vn.outputs.vn }}.tar.gz
-        path: dnmtools-${{ steps.vn.outputs.vn }}.tar.gz
     - name: make distcheck
       run: make -j4 distcheck

CPPLINT.cfg

@@ -1,24 +1,18 @@
-# MIT License
+# This file is part of dnmtools
 #
-# Copyright (c) 2025 Andrew Smith
+# Copyright (C) 2023-2025 Andrew D. Smith
 #
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
+# Authors: Andrew D. Smith
 #
-# The above copyright notice and this permission notice shall be included in all
-# copies or substantial portions of the Software.
+# This 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.
 #
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-# SOFTWARE.
+# This software 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.
 set noparent
 filter=-runtime/references
 filter=-build/include_subdir

Makefile.am

@@ -22,7 +22,13 @@ ACLOCAL_AMFLAGS = -I m4
 
 SUBDIRS := src/smithlab_cpp src/abismal
 install installdirs: SUBDIRS := $(filter-out src/smithlab_cpp src/abismal, $(SUBDIRS))
-AM_CPPFLAGS = -I $(top_srcdir)/src/common -I $(top_srcdir)/src/smithlab_cpp -I $(top_srcdir)/src/bamxx
+AM_CPPFLAGS = \
+	-I $(top_srcdir)/src/common \
+	-I $(top_srcdir)/src/smithlab_cpp \
+	-I $(top_srcdir)/src/bamxx
+if BUILD_NANOPORE
+AM_CPPFLAGS += -DBUILD_NANOPORE
+endif
 
 AM_CXXFLAGS = -Wall -Wextra -Wpedantic -Wno-unknown-attributes
 
@@ -168,9 +174,9 @@ libdnmtools_a_SOURCES = \
 	src/common/dnmtools_utils.cpp
 
 libdnmtools_a_SOURCES += \
+        src/common/dnmtools_lgamma.hpp \
         src/common/Interval.hpp \
         src/common/Interval6.hpp \
-	src/bamxx/bamxx.hpp \
         src/common/dnmtools_gaussinv.hpp \
 	src/common/bam_record_utils.hpp \
 	src/common/counts_header.hpp \
@@ -190,14 +196,17 @@ libdnmtools_a_SOURCES += \
         src/common/dnmtools_utils.hpp \
         src/common/dnmt_error.hpp
 
+libdnmtools_a_SOURCES += \
+	src/bamxx/bamxx.hpp \
+	src/common/nlohmann/json.hpp
+
 # ADS: additional radmeth sources to help isolate the parts using GSL for
 # optimization
 libdnmtools_a_SOURCES += \
         src/radmeth/radmeth_optimize_series.hpp \
         src/radmeth/radmeth_optimize_gamma.hpp \
         src/radmeth/radmeth_optimize_params.hpp \
         src/radmeth/radmeth_model.hpp \
-        src/radmeth/radmeth_lgamma.hpp \
         src/radmeth/radmeth_utils.hpp \
         src/radmeth/radmeth_design.hpp
 

cmake/FindHTSLIB.cmake

@@ -117,6 +117,17 @@ if(HTSLIB_INCLUDE_DIR AND EXISTS "${HTSLIB_INCLUDE_DIR}/htslib/hts.h")
     set(HTSLIB_VERSION_MINOR "")
     set(HTSLIB_VERSION_PATCH "")
   endif()
+
+  # Make sure the version numbers don't have leading zeros
+  # The minor version is encoded in such a way that it often will
+  foreach(part HTSLIB_VERSION_MAJOR HTSLIB_VERSION_MINOR HTSLIB_VERSION_PATCH)
+    if(${${part}} MATCHES "^[0]+$")
+      set(${part} "0")
+    else()
+      string(REGEX REPLACE "^0+" "" ${part} "${${part}}")
+    endif()
+  endforeach()
+
   # Set canonical variables
   set(HTSLIB_MAJOR_VERSION "${HTSLIB_VERSION_MAJOR}")
   set(HTSLIB_MINOR_VERSION "${HTSLIB_VERSION_MINOR}")

configure.ac

@@ -55,6 +55,11 @@ AC_ARG_WITH([libdeflate],
   [AS_HELP_STRING([--with-libdeflate], [use libdeflate for BAM output])],
   [with_libdeflate=yes], [with_libdeflate=no])
 
+dnl arg for building with mods support in 'counts'
+AC_ARG_WITH([htsmods],
+  [AS_HELP_STRING([--with-htsmods], [use HTSLib 'mods' to support Nanopore])],
+  [with_htsmods=yes], [with_htsmods=no])
+
 dnl check for required libraries
 AC_SEARCH_LIBS([pthread_create], [pthread], [], [AC_MSG_FAILURE(["pthread library not found"])])
 AC_SEARCH_LIBS([gzopen], [z], [], [AC_MSG_FAILURE(["Zlib library not found"])])
@@ -64,6 +69,41 @@ AS_IF([test "x$with_libdeflate" = "xyes"],
                    [AC_MSG_ERROR([--with-libdeflate specified but libdeflate not found])])
   ])
 AC_SEARCH_LIBS([hts_version], [hts], [], [AC_MSG_FAILURE([$hts_fail_msg])])
+AC_CHECK_HEADERS([htslib/hts.h], [], [AC_MSG_ERROR([hts.h not found])])
+# Require HTS_VERSION >= 102000
+AS_IF([test "x$with_htsmods" = "xyes"],
+  [
+    AC_COMPILE_IFELSE(
+      [
+        AC_LANG_PROGRAM([[
+          #include <htslib/hts.h>
+          #if !defined(HTS_VERSION)
+          # error HTS_VERSION not defined
+          #endif
+          #if HTS_VERSION < 102000
+          # error htslib library too old
+          #endif
+        ]], [[]])
+      ], [have_htsmods_version=yes], [have_htsmods_version=no])
+  ],
+  [have_htsmods_version=yes]
+)
+
+AC_COMPUTE_INT(
+  [hts_version_macro],
+  [HTS_VERSION],
+  [#include <htslib/hts.h>],
+  [AC_MSG_ERROR([Could not compute HTS_VERSION])]
+)
+AC_MSG_NOTICE([Detected htslib version: $hts_version_macro])
+
+AS_IF([test "x$have_htsmods_version" != "xyes"], [
+  AC_MSG_ERROR([
+    HTSLib version must be at least 102000 (v1.20) for mods support
+  ])
+])
+AM_CONDITIONAL([BUILD_NANOPORE], [test "x$with_htsmods" = "xyes"])
+
 AC_SEARCH_LIBS([cblas_dgemm], [gslcblas], [], [AC_MSG_FAILURE([$gsl_fail_msg])])
 AC_SEARCH_LIBS([gsl_blas_dgemm], [gsl], [], [AC_MSG_FAILURE([$gsl_fail_msg])])
 

data/LICENSE

@@ -17,8 +17,8 @@ details.
 ========================================================================
 
 Additional licenses/copyrights that apply to DNMTools pre-built binaries,
-which link statically to GSL (GNU Scientific Library), ZLib, HTSlib and
-libdeflate.
+which link statically to GSL (GNU Scientific Library), ZLib, HTSlib,
+libdeflate and Niels Lohmann's JSON library.
 
 ========================================================================
 GNU Scientific Library
@@ -125,3 +125,28 @@ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
+
+========================================================================
+JSON
+
+MIT License
+
+Copyright (c) 2013-2025 Niels Lohmann
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

src/CMakeLists.txt

@@ -13,7 +13,15 @@
 # You should have received a copy of the GNU General Public License along with
 # this program. If not, see <https://www.gnu.org/licenses/>.
 
-if(NOT TARGET smithlab_cpp)
+if(BUILD_NANOPORE)
+  find_package(HTSLIB 1.20 REQUIRED)
+  add_compile_definitions(BUILD_NANOPORE)
+else()
+  find_package(HTSLIB REQUIRED)
+endif()
+find_package(Threads REQUIRED)
+
+if(NOT TARGET bamxx)
   add_subdirectory(bamxx)
 endif()
 if(NOT TARGET smithlab_cpp)
@@ -32,43 +40,10 @@ add_executable(dnmtools dnmtools.cpp)
 target_include_directories(dnmtools PUBLIC ${CMAKE_BINARY_DIR})
 target_link_libraries(dnmtools PUBLIC
   dnmtools_objs
-  smithlab_cpp
-  bamxx
   abismal_objs
-  radmeth
-  format-reads
-  uniq
-  bsrate
-  methcounts
-  nanopore
-  symmetric-cpgs
-  levels
-  methsummary
-  hmr
-  hmr-rep
-  hypermr
-  methentropy
-  pmd
-  roimethstat
-  autocorr
-  cpgbins
-  multimethstat
-  mlml
-  methstates
-  allelicmeth
-  amrfinder
-  amrtester
-  fast-liftover
-  metagene
-  lift-filter
-  clean-hairpins
-  guessprotocol
-  merge-bsrate
-  merge-methcounts
-  covered
-  recovered
-  xcounts
-  unxcounts
-  selectsites
-  kmersites
+  dnmtools_analysis_objs
+  dnmtools_utils_objs
+  dnmtools_radmeth_objs
+  dnmtools_mlml_objs
+  dnmtools_amrfinder_objs
 )