Merge pull request #78 from smithlabcode/submodule-update

Several major updates

Author: andrewdavidsmith

.cppcheck_suppress

@@ -0,0 +1,23 @@
+# This file is part of preseq
+#
+# Copyright (C) 2024: Andrew D. Smith
+#
+# 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 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
+checkersReport
+unusedFunction:src/bam_record_utils.hpp
+unusedFunction:src/bam_record_utils.cpp
+*:src/smithlab_cpp*
+unusedStructMember:src/*.hpp

.github/workflows/cppcheck.yml

@@ -0,0 +1,54 @@
+# This file is part of preseq
+#
+# Copyright (C) 2024: Andrew D. Smith
+#
+# 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 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.
+
+name: Linting with cppcheck
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+  workflow_dispatch:
+
+jobs:
+  cppcheck:
+    runs-on: ubuntu-24.04
+    strategy:
+      matrix:
+        python-version: ["3.12"]
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Python setup ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install cppcheck
+      run: |
+        conda install -c conda-forge cppcheck
+
+    - name: Run cppcheck
+      run: |
+        ${CONDA}/bin/cppcheck \
+          --std=c++17 \
+          --enable=all \
+          --check-level=exhaustive \
+          --suppressions-list=.cppcheck_suppress \
+          -I src/smithlab_cpp \
+          $(git ls-files '*.*pp')

.github/workflows/cpplint.yml

@@ -44,9 +44,6 @@ jobs:
         python -m pip install --upgrade pip
         pip install cpplint
 
-    - name: Check cpplint version
-      run: cpplint --version
-
     - name: Run cpplint
       run: |
         cpplint --quiet --repository=. $(git ls-files '*.*pp')

.gitmodules

@@ -4,3 +4,6 @@
 [submodule "src/smithlab_cpp"]
 	path = src/smithlab_cpp
 	url = ../smithlab_cpp.git
+[submodule "src/bamxx"]
+	path = src/bamxx
+	url = ../bamxx.git

Makefile.am

@@ -18,10 +18,10 @@ ACLOCAL_AMFLAGS = -I m4
 
 SUBDIRS := src/smithlab_cpp
 install installdirs: SUBDIRS := $(filter-out src/smithlab_cpp, $(SUBDIRS))
-AM_CPPFLAGS = -I $(top_srcdir)/src/smithlab_cpp
+AM_CPPFLAGS = -I $(top_srcdir)/src/smithlab_cpp -I $(top_srcdir)/src/bamxx
 AM_CPPFLAGS += -Wall -Wextra -Wpedantic -Wno-unknown-attributes
 
-CXXFLAGS = -O2 # default has optimization on
+CXXFLAGS = -O2 -DNDEBUG # default w/ optimization; careful for math
 
 EXTRA_DIST = \
 	README.md \
@@ -48,7 +48,6 @@ LDADD = src/smithlab_cpp/libsmithlab_cpp.a
 
 bin_PROGRAMS = preseq
 if ENABLE_HTS
-bin_PROGRAMS += to-mr
 AM_CPPFLAGS += -DHAVE_HTSLIB
 endif
 
@@ -64,14 +63,14 @@ preseq_SOURCES = \
         src/lc_extrap.cpp \
         src/bound_pop.hpp \
         src/bound_pop.cpp \
+        src/bamxx/bamxx.hpp \
         src/pop_size.hpp \
         src/pop_size.cpp \
         src/continued_fraction.hpp \
         src/continued_fraction.cpp \
+        src/bam_record_utils.hpp \
+        src/bam_record_utils.cpp \
         src/load_data_for_complexity.hpp \
         src/load_data_for_complexity.cpp \
         src/moment_sequence.hpp \
         src/moment_sequence.cpp
-
-to_mr_SOURCES = \
-        src/to-mr.cpp