Adding cmake and static analysis - #81

Merged

andrewdavidsmith merged 92 commits into

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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7352e80
src/CLI11.hpp: adding CLI11
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13a0553
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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111ae40
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

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