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Merged
andrewdavidsmith merged 106 commits into from
Nov 25, 2025
Merged

Adding static analysis setup #312

andrewdavidsmith merged 106 commits into from
Nov 25, 2025

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@andrewdavidsmith
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@andrewdavidsmith andrewdavidsmith commented Nov 25, 2025

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@andrewdavidsmith
src/amrfinder/allelicmeth.cpp: changes to add static analysis
9da5c2e
@andrewdavidsmith
src/amrfinder/amrfinder.cpp: changes to add static analysis
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@andrewdavidsmith
src/amrfinder/amrtester.cpp: changes to add static analysis
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@andrewdavidsmith
src/analysis/autocorr.cpp: changes to add static analysis
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@andrewdavidsmith
src/analysis/bsrate.cpp: changes to add static analysis
f45e454
@andrewdavidsmith
src/analysis/cpgbins.cpp: changes to add static analysis
fc99436
@andrewdavidsmith
src/analysis/hmr-rep.cpp: changes to add static analysis
d5024b9
@andrewdavidsmith
src/analysis/hmr.cpp: changes to add static analysis
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@andrewdavidsmith
src/analysis/hypermr.cpp: changes to add static analysis
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@andrewdavidsmith
src/analysis/levels.cpp: changes to add static analysis
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@andrewdavidsmith
src/analysis/metagene.cpp: changes to add static analysis
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@andrewdavidsmith
src/analysis/methcounts.cpp: changes to add static analysis
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@andrewdavidsmith
src/analysis/methentropy.cpp: changes to add static analysis
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@andrewdavidsmith
src/analysis/methstates.cpp: changes to add static analysis
c2fcf3a
@andrewdavidsmith
src/analysis/multimethstat.cpp: changes to add static analysis
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@andrewdavidsmith
src/analysis/nanopore.cpp: changes to add static analysis
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@andrewdavidsmith
src/analysis/pmd.cpp: changes to add static analysis
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@andrewdavidsmith
src/analysis/roimethstat.cpp: changes to add static analysis
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@andrewdavidsmith
src/common/BetaBin.cpp: changes to add static analysis
9c61cba
@andrewdavidsmith
src/common/BetaBin.hpp: changes to add static analysis
ec17833
@andrewdavidsmith
src/common/EmissionDistribution.cpp: changes to add static analysis
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@andrewdavidsmith
src/common/EmissionDistribution.hpp: changes to add static analysis
fc09428
@andrewdavidsmith
src/common/Epiread.cpp: changes to add static analysis
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@andrewdavidsmith
src/common/Epiread.hpp: changes to add static analysis
cc0795b
@andrewdavidsmith
src/common/EpireadStats.cpp: changes to add static analysis
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@andrewdavidsmith
src/common/EpireadStats.hpp: changes to add static analysis
9d32587
@andrewdavidsmith
src/common/Interval.cpp: changes to add static analysis
c2af9dd
@andrewdavidsmith
src/common/Interval6.cpp: changes to add static analysis
a7af157
@andrewdavidsmith
src/common/LevelsCounter.cpp: changes to add static analysis
5aa4694
@andrewdavidsmith
src/common/LevelsCounter.hpp: changes to add static analysis
9dcd30d
@andrewdavidsmith
src/utils/uniq.cpp: changes to add static analysis
c135b74
@andrewdavidsmith
src/utils/unxcounts.cpp: changes to add static analysis
9e6620c
@andrewdavidsmith
src/utils/xcounts.cpp: changes to add static analysis
9942822
@andrewdavidsmith
adding static analysis config files
75f078c
@andrewdavidsmith
cmake/FindHTSLIB.cmake cmake/static_analysis.cmake: adding the cmake …
e07a63d 
…files for htslib and static analysis
@andrewdavidsmith
cmake/static_analysis.cmake: removing the hints for iwyu
3576d9e
@andrewdavidsmith
src/amrfinder/CMakeLists.txt: adding this cmake
dc7d5f6
@andrewdavidsmith
src/amrfinder/allelicmeth.cpp: linting
3bbe729
@andrewdavidsmith
src/common/EpireadStats.hpp: adding a size function for std::size()
c8a9f87
@andrewdavidsmith
src/amrfinder/amrfinder.cpp: linting
8a2edba
@andrewdavidsmith
src/amrfinder/amrtester.cpp: linting
bdd438b
@andrewdavidsmith
Adding CMakeLists.txt files
c88f69f
@andrewdavidsmith
data/config.h.in: adding file
9423830
@andrewdavidsmith
src/amrfinder/amrfinder.cpp: more linting
e9e0b23
@andrewdavidsmith
src/amrfinder/amrtester.cpp: more linting
40132be
@andrewdavidsmith
src/mlml/CMakeLists.txt: adding
cbac212
@andrewdavidsmith
src/common/CMakeLists.txt: adding GSL dependency in cmake
03473c3
@andrewdavidsmith
src/CMakeLists.txt: Adding all the deps dnmtools binary
72f848d
@andrewdavidsmith
src/mlml/mlml.cpp: linting
e681b86
@andrewdavidsmith
src/mlml/mlml.cpp: more linting
3808dcc
@andrewdavidsmith
src/dnmtools.cpp: more linting
3b6569a
@andrewdavidsmith
src/amrfinder/amrfinder.cpp: removing dead code
792757c
@andrewdavidsmith
src/common/EpireadStats.cpp: removing commented deadcode
04cf61b
@andrewdavidsmith
src/radmeth/radmeth_design.cpp: removing commented deadcode
4d9fce3
@andrewdavidsmith
src/utils/merge-methcounts.cpp: removing commented deadcode
e210954
@andrewdavidsmith
src/radmeth/CMakeLists.txt: removing commented deadcode
4c6ae5d
@andrewdavidsmith
src/analysis/pmd.cpp: removing commented deadcode
ac787ce
@andrewdavidsmith
src/common/EpireadStats.cpp: fixing bug with log_likelihood function …
326626c 
…signature
@andrewdavidsmith andrewdavidsmith merged commit 326626c into master Nov 25, 2025
5 checks passed
@andrewdavidsmith andrewdavidsmith deleted the adding-static-analysis branch November 27, 2025 00:20
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@andrewdavidsmith