Adding cmake and static analysis - #81

Open

andrewdavidsmith wants to merge 92 commits into

adding-cmake-and-static-analysis

Commits on Dec 5, 2025

linting config files: adding and updating
andrewdavidsmith
committed
686d028
cmake/static_analysis.cmake and cmake/FindHTSLIB.cmake: adding cmake files
andrewdavidsmith
committed
0f4c5fc
src/bam_record_utils.hcpp: linting
andrewdavidsmith
committed
7352e80
src/CLI11.hpp: adding CLI11
andrewdavidsmith
committed
13a0553
src/load_data_for_complexity.cpp: linting
andrewdavidsmith
committed
89d9289
switching to CLI11
andrewdavidsmith
committed
dbddb7e
src/common.hcpp: formatting and adding some utilities
andrewdavidsmith
committed
bb1e19d
src/continued_fraction.hcpp: linting
andrewdavidsmith
committed
7bbbc44
src/moment_sequence.hcpp: linting
andrewdavidsmith
committed
5cc36ee
src/preseq.cpp: iwyu and formatting
andrewdavidsmith
committed
6bdb215
src/bamxx and src/smithlab_cpp: updating submodules
andrewdavidsmith
committed
111ae40
data/config.h.in: adding this for cmake builds
andrewdavidsmith
committed
5c19dd0
CMakeLists.txt src/CMakeLists.txt: adding cmake stuff
andrewdavidsmith
committed
b92450f
src/CMakeLists.txt: htslib stuff is only included in build if htslib is specified
andrewdavidsmith
committed
752d6ec
src/CMakeLists.txt: removing requirement on particular version for htslib
andrewdavidsmith
committed
9060f06
src/bound_pop.cpp: linting and formatting help output
andrewdavidsmith
committed
02ed726
src/c_curve.cpp: linting and formatting help output
andrewdavidsmith
committed
ec00148
src/common.hpp: linting and deadcode
andrewdavidsmith
committed
67ee2d3
src/gc_extrap.cpp: linting and formatting help output
andrewdavidsmith
committed
40e2633
src/pop_size.cpp: linting and formatting help output
andrewdavidsmith
committed
e0593dd
src/lc_extrap.cpp: linting and formatting help output
andrewdavidsmith
committed
2d2f554
src/load_data_for_complexity.cpp: linting
andrewdavidsmith
committed
6bbd303
src/preseq.cpp: fixing the args passed to subcommands
andrewdavidsmith
committed
1d64343
tests/scripts several scripts: updating args to have -i explicit
andrewdavidsmith
committed
5e924e7
src/CLI11/CLI11.hpp: moving file
andrewdavidsmith
committed
3d339d8
Adding license and cpplint config for cli11
andrewdavidsmith
committed
f59363d

Commits on Dec 6, 2025

Commits on Dec 11, 2025

src/load_data_for_complexity.cpp: fixing do-while loops
andrewdavidsmith
committed
2289cfe
src/load_data_for_complexity.cpp: cleanup
andrewdavidsmith
committed
8d72975
src/dnmt_error.hpp: no longer needed
andrewdavidsmith
committed
53bc550
src/bam_record_utils.hcpp: linting
andrewdavidsmith
committed
7ab093d
.clang-format-ignore: adding
andrewdavidsmith
committed
24b518f
src/smithlab_cpp: removing submodule
andrewdavidsmith
committed
99700c4
.gitmodules: removing smithlab_cpp
andrewdavidsmith
committed
7bd447c
src/Interval6.hcpp: adding
andrewdavidsmith
committed
b64c015
src/CMakeLists.txt: removing smithlab_cpp and adding Interval6
andrewdavidsmith
committed
9e8e149
multiple sources: renaming functions
andrewdavidsmith
committed
55c6047
src/load_data_for_complexity.hcpp: some simplification
andrewdavidsmith
committed
9f60d2f
src/gc_extrap.cpp: removed option for input being MappedRead format
andrewdavidsmith
committed
245abed

Commits on Dec 12, 2025

Commits on Dec 13, 2025

Commits on Dec 24, 2025

configure.ac: making htslib on by default and adding check for libdeflate
andrewdavidsmith
committed
b514a9c
src/c_curve.cpp: updating args with default values
andrewdavidsmith
committed
7bcf82e
src/common.cpp: requiring an output file in writing ptredicted complexity curve
andrewdavidsmith
committed
ca11a12
src/gc_extrap.cpp: updating default arg values
andrewdavidsmith
committed
aac09d4
src/lc_extrap.cpp: updating default arg values and arg flags for consistency
andrewdavidsmith
committed
a637851
documentation/README.md: update
andrewdavidsmith
committed
fd317a4
tests/data/gc_extrap_input.mr to bed: changing file format
andrewdavidsmith
committed
01ee79a
Makefile.am: renaming test data file
andrewdavidsmith
committed
0b37c54
configure.ac: fixing type
andrewdavidsmith
committed
e47f668
m4/ax_pthread.m4: adding macro to find the proper threads lib
andrewdavidsmith
committed
262272d
Makefile.am: ENABLE_HTS to ENABLE_HTSLIB
andrewdavidsmith
committed
dddd4f0
configure.ac: more detailed config...
andrewdavidsmith
committed
be82d67
configure.ac: adding checks for additional dependencies when building against htslib
andrewdavidsmith
committed
a28a192
src/nlohmann/LICENSE: adding license
andrewdavidsmith
committed
f8cb361
src/nlohmann/CPPLINT.cfg: adding CPPLINT.cfg to disable cpplint
andrewdavidsmith
committed
4153529
linting
andrewdavidsmith
committed
041de2b
adding include guard
andrewdavidsmith
committed
f14a34f