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Adding cmake and static analysis - #81

Merged

andrewdavidsmith merged 92 commits into

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adding-cmake-and-static-analysis

Aug 26, 2026

Commits on Dec 5, 2025
- linting config files: adding and updating
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  686d028
- cmake/static_analysis.cmake and cmake/FindHTSLIB.cmake: adding cmake files
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  0f4c5fc
- src/bam_record_utils.hcpp: linting
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- src/CLI11.hpp: adding CLI11
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- src/load_data_for_complexity.cpp: linting
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  89d9289
- switching to CLI11
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  dbddb7e
- src/common.hcpp: formatting and adding some utilities
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  bb1e19d
- src/continued_fraction.hcpp: linting
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  7bbbc44
- src/moment_sequence.hcpp: linting
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  5cc36ee
- src/preseq.cpp: iwyu and formatting
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  6bdb215
- src/bamxx and src/smithlab_cpp: updating submodules
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- data/config.h.in: adding this for cmake builds
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  5c19dd0
- CMakeLists.txt src/CMakeLists.txt: adding cmake stuff
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  b92450f
- src/CMakeLists.txt: htslib stuff is only included in build if htslib is specified
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  752d6ec
- src/CMakeLists.txt: removing requirement on particular version for htslib
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  9060f06
- src/bound_pop.cpp: linting and formatting help output
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  02ed726
- src/c_curve.cpp: linting and formatting help output
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  ec00148
- src/common.hpp: linting and deadcode
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  67ee2d3
- src/gc_extrap.cpp: linting and formatting help output
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  40e2633
- src/pop_size.cpp: linting and formatting help output
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  e0593dd
- src/lc_extrap.cpp: linting and formatting help output
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  2d2f554
- src/load_data_for_complexity.cpp: linting
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  6bbd303
- src/preseq.cpp: fixing the args passed to subcommands
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  1d64343
- tests/scripts several scripts: updating args to have -i explicit
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  5e924e7
- src/CLI11/CLI11.hpp: moving file
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  3d339d8
- Adding license and cpplint config for cli11
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  f59363d
Commits on Dec 6, 2025
- .cppcheck_suppress: adding CLI11.hpp to suppression list
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  31994a0
- src/bound_pop.cpp: linting
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  9cbc563
- src/c_curve.cpp: linting
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  4ed726b
- src/common.hcpp: linting
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  8ca97eb
- multiple sources: linting
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  d0dbcb4
- src/load_data_for_complexity.cpp: linting
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  51b4ebe
Commits on Dec 11, 2025
- src/load_data_for_complexity.cpp: fixing do-while loops
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  2289cfe
- src/load_data_for_complexity.cpp: cleanup
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  8d72975
- src/dnmt_error.hpp: no longer needed
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  53bc550
- src/bam_record_utils.hcpp: linting
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  7ab093d
- .clang-format-ignore: adding
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  24b518f
- src/smithlab_cpp: removing submodule
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  99700c4
- .gitmodules: removing smithlab_cpp
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  7bd447c
- src/Interval6.hcpp: adding
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  b64c015
- src/CMakeLists.txt: removing smithlab_cpp and adding Interval6
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  9e8e149
- multiple sources: renaming functions
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  55c6047
- src/load_data_for_complexity.hcpp: some simplification
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  9f60d2f
- src/gc_extrap.cpp: removed option for input being MappedRead format
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  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
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  b514a9c
- src/c_curve.cpp: updating args with default values
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  7bcf82e
- src/common.cpp: requiring an output file in writing ptredicted complexity curve
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  ca11a12
- src/gc_extrap.cpp: updating default arg values
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  aac09d4
- src/lc_extrap.cpp: updating default arg values and arg flags for consistency
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  a637851
- documentation/README.md: update
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  fd317a4
- tests/data/gc_extrap_input.mr to bed: changing file format
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  01ee79a
- Makefile.am: renaming test data file
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  0b37c54
- configure.ac: fixing type
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  e47f668
- m4/ax_pthread.m4: adding macro to find the proper threads lib
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  262272d
- Makefile.am: ENABLE_HTS to ENABLE_HTSLIB
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  dddd4f0
- configure.ac: more detailed config...
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  be82d67
- configure.ac: adding checks for additional dependencies when building against htslib
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  a28a192
- src/nlohmann/LICENSE: adding license
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  f8cb361
- src/nlohmann/CPPLINT.cfg: adding CPPLINT.cfg to disable cpplint
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  4153529
- linting
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  041de2b
- adding include guard
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  f14a34f

Commits

Commits on Dec 5, 2025

Commits on Dec 6, 2025

Commits on Dec 11, 2025

Commits on Dec 12, 2025

Commits on Dec 13, 2025

Commits on Dec 24, 2025