Merge pull request #321 from smithlabcode/summary-analysis

Adding a commant to do multiple analysis that all process the same BAM file

Author: andrewdavidsmith

.cppcheck_suppress

@@ -32,12 +32,8 @@ unusedStructMember
 # Ignore missing includes because if they are real things won't build
 missingInclude
 # Exclude external files
-*:*CLI11.hpp
-*:*json.hpp
-*:*asio*
 *:*smithlab_cpp*
-*:*ssl.hpp
-*:*indicators.hpp
+*:*popcnt.hpp
 # Problem caused by external files
 toomanyconfigs
 # More problems caused by external files -- with too many ifdefs

CMakeLists.txt

@@ -4,15 +4,15 @@
 #
 # Authors: Andrew D. Smith
 #
-# 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.
+# 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.
 #
-# 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.
+# 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.
 
 # to find the version of cmake do
 # $ cmake --version
@@ -41,96 +41,6 @@ list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake")
 
 configure_file(data/config.h.in config.h)
 
-# Collect any global linker options as needed and then apply them
-# individually to targets
-set(GLOBAL_COMPILE_OPTIONS "")
-set(GLOBAL_LINKER_OPTIONS "")
-
-if(USE_STATIC_LIBS)
-  # This needs to come before finding any libraries so that the static
-  # versions are identified
-  message(STATUS "Enabling static linkage for all non-system libraries")
-  message(STATUS "Configuring to clone ZLib")
-  include(ExternalProject)
-  set(ZLIB_CMAKE_ARGS
-    -DZLIB_BUILD_EXAMPLES=off
-    -DSKIP_INSTALL_FILES=on
-    -DCMAKE_POSITION_INDEPENDENT_CODE=on
-    -DCMAKE_INSTALL_PREFIX=${PROJECT_BINARY_DIR}/src/zlib
-    -DCMAKE_BUILD_TYPE=Release
-  )
-  if(CMAKE_SYSTEM_NAME STREQUAL "Darwin")
-    list(APPEND ZLIB_CMAKE_ARGS
-      -DCMAKE_OSX_DEPLOYMENT_TARGET=${CMAKE_OSX_DEPLOYMENT_TARGET}
-    )
-  endif()
-  ExternalProject_Add(
-    ZLIB
-    GIT_REPOSITORY https://github.com/madler/zlib.git
-    GIT_TAG master
-    CMAKE_ARGS ${ZLIB_CMAKE_ARGS}
-  )
-  # Include the built zlib headers and link against the built zlib library
-  set(ZLIB_INCLUDE_DIR "${PROJECT_BINARY_DIR}/src/zlib/include")
-  set(ZLIB_LIBRARY "${PROJECT_BINARY_DIR}/src/zlib/lib/libz.a")
-
-  # Create the CMake target for the built zlib
-  add_library(ZLIB_IMPORTED INTERFACE)
-  set_target_properties(ZLIB_IMPORTED PROPERTIES
-    INTERFACE_INCLUDE_DIRECTORIES ${ZLIB_INCLUDE_DIR}
-    INTERFACE_LINK_LIBRARIES ${ZLIB_LIBRARY}
-  )
-
-  # This alias means we don't need to worry where zlib came from
-  add_library(ZLIB::ZLIB ALIAS ZLIB_IMPORTED)
-
-  ExternalProject_Add(
-    HTSLIB
-    GIT_REPOSITORY https://github.com/samtools/htslib.git
-    GIT_TAG master
-    CONFIGURE_COMMAND ""
-    # "autoreconf -i <SOURCE_DIR>; <SOURCE_DIR>/configure"
-    BUILD_COMMAND make -C <SOURCE_DIR> lib-static -j
-    INSTALL_COMMAND ""
-    # make install
-    TEST_COMMAND ""
-    BUILD_BYPRODUCTS libhts.a
-  )
-  # ExternalProject_Add_Step(HTSLIB
-  #   bootstrap
-  #   COMMAND autoreconf -i <SOURCE_DIR>
-  #   DEPENDEES download
-  #   DEPENDERS configure
-  # )
-  ExternalProject_Get_Property(HTSLIB SOURCE_DIR)
-  message(STATUS "SOURCE_DIR: ${SOURCE_DIR}")
-
-  # Include the built zlib headers and link against the built zlib library
-  set(HTSLIB_INCLUDE_DIR "${SOURCE_DIR}/src/htslib/htslib")
-  set(HTSLIB_LIBRARY "${SOURCE_DIR}/htslib.a")
-
-  # Create the CMake target for the built zlib
-  add_library(HTSLIB_IMPORTED INTERFACE)
-  set_target_properties(HTSLIB_IMPORTED PROPERTIES
-    INTERFACE_INCLUDE_DIRECTORIES ${HTSLIB_INCLUDE_DIR}
-    INTERFACE_LINK_LIBRARIES ${HTSLIB_LIBRARY}
-  )
-  set_target_properties(HTSLIB_IMPORTED PROPERTIES IMPORTED_LOCATION ${HTSLIB_LIBRARY})
-
-  # This alias means we don't need to worry where htslib came from
-  add_library(HTSLIB::HTSLIB ALIAS HTSLIB_IMPORTED)
-
-  # Set static for the linker so the compiler's libraries will be static
-  ## ADS: using this instead of forcing -static for everything avoids the
-  ## static linkage that Aiso warns against, but also means it's not 100%
-  ## static linked ADS: can't do this if the compiler is AppleClang because
-  ## they don't have the libc++.a and the libgcc wouldn't make sense anyway.
-  if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")  # macOS
-    list(APPEND GLOBAL_LINKER_OPTIONS -static-libgcc -static-libstdc++)
-  endif()
-
-endif()
-
 if(ENABLE_LTO)
   # Turn on LTO if we are building for distribution
   include(CheckIPOSupported)
@@ -147,17 +57,12 @@ if(STATIC_ANALYSIS)
 endif()
 
 # ADS: set the most stringent warnings we can
-list(APPEND GLOBAL_COMPILE_OPTIONS
-  -Wall -Wextra -Wpedantic -Werror -Wfatal-errors
+add_compile_options(
+  -Wall
+  -Wextra
+  -Wpedantic
+  -Werror
+  -Wfatal-errors
 )
 
-if(STRIP_PATHS_FROM_BINARIES)
-  # This is set if we have configured to distribute
-  set(PREFIX_MAP_ARG -ffile-prefix-map=)
-  list(TRANSFORM STRIP_SUB_LIST PREPEND ${PREFIX_MAP_ARG})
-  list(APPEND GLOBAL_COMPILE_OPTIONS ${STRIP_SUB_LIST})
-endif()
-
-message(STATUS "Finished global compile and linker configuration")
-
 add_subdirectory(src)

Makefile.am

@@ -222,6 +222,7 @@ dnmtools_SOURCES += src/analysis/levels.cpp
 dnmtools_SOURCES += src/analysis/hypermr.cpp
 dnmtools_SOURCES += src/analysis/metagene.cpp
 dnmtools_SOURCES += src/analysis/autocorr.cpp
+dnmtools_SOURCES += src/analysis/methsummary.cpp
 
 dnmtools_SOURCES += src/utils/clean-hairpins.cpp
 dnmtools_SOURCES += src/utils/guessprotocol.cpp

src/CMakeLists.txt

@@ -43,6 +43,7 @@ target_link_libraries(dnmtools PUBLIC
   nanopore
   symmetric-cpgs
   levels
+  methsummary
   hmr
   hmr-rep
   hypermr

src/abismal

@@ -89,7 +89,7 @@ find_first_epiread_ending_after_position(const string &query_chrom,
     backup_to_start_of_current_record(in);
 
     // we've hit the end of file without finding an epiread
-    if (low_pos == eof - 2)
+    if (low_pos + 2 == static_cast<std::streamoff>(eof))
       return -1;
 
     if (!(in >> chrom >> start >> seq)) {

src/amrfinder/amrtester.cpp

@@ -121,6 +121,9 @@ main_levels(int argc, char *argv[]) {  // NOLINT(*-avoid-c-arrays)
     const std::string meth_file = leftover_args.front();
     /****************** END COMMAND LINE OPTIONS *****************/
 
+    if (relaxed_mode)
+      MSite::no_extra_fields = false;
+
     if (!is_msite_file(meth_file))
       throw std::runtime_error{"malformed counts file: " + meth_file};