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smithlabcode / dnmtools Public

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Adding static analysis setup#312

Merged

andrewdavidsmith merged 106 commits intomastersmithlabcode/dnmtools:masterfrom

adding-static-analysissmithlabcode/dnmtools:adding-static-analysisCopy head branch name to clipboard

Nov 25, 2025

Conversation Commits106 (106)Checks Files changed

Merged

Adding static analysis setup#312
andrewdavidsmith merged 106 commits intomasterfrom
adding-static-analysis

Commits

Commits on Nov 25, 2025

src/amrfinder/allelicmeth.cpp: changes to add static analysis
andrewdavidsmith
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src/amrfinder/amrfinder.cpp: changes to add static analysis
andrewdavidsmith
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src/amrfinder/amrtester.cpp: changes to add static analysis
andrewdavidsmith
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src/analysis/autocorr.cpp: changes to add static analysis
andrewdavidsmith
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src/analysis/bsrate.cpp: changes to add static analysis
andrewdavidsmith
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src/analysis/cpgbins.cpp: changes to add static analysis
andrewdavidsmith
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src/analysis/hmr-rep.cpp: changes to add static analysis
andrewdavidsmith
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src/analysis/hmr.cpp: changes to add static analysis
andrewdavidsmith
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src/analysis/hypermr.cpp: changes to add static analysis
andrewdavidsmith
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src/analysis/levels.cpp: changes to add static analysis
andrewdavidsmith
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src/analysis/metagene.cpp: changes to add static analysis
andrewdavidsmith
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src/analysis/methcounts.cpp: changes to add static analysis
andrewdavidsmith
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src/analysis/methentropy.cpp: changes to add static analysis
andrewdavidsmith
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src/analysis/methstates.cpp: changes to add static analysis
andrewdavidsmith
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src/analysis/multimethstat.cpp: changes to add static analysis
andrewdavidsmith
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src/analysis/nanopore.cpp: changes to add static analysis
andrewdavidsmith
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src/analysis/pmd.cpp: changes to add static analysis
andrewdavidsmith
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src/analysis/roimethstat.cpp: changes to add static analysis
andrewdavidsmith
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src/common/BetaBin.cpp: changes to add static analysis
andrewdavidsmith
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src/common/BetaBin.hpp: changes to add static analysis
andrewdavidsmith
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src/common/EmissionDistribution.cpp: changes to add static analysis
andrewdavidsmith
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src/common/EmissionDistribution.hpp: changes to add static analysis
andrewdavidsmith
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src/common/Epiread.cpp: changes to add static analysis
andrewdavidsmith
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src/common/Epiread.hpp: changes to add static analysis
andrewdavidsmith
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src/common/EpireadStats.cpp: changes to add static analysis
andrewdavidsmith
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src/common/EpireadStats.hpp: changes to add static analysis
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src/common/Interval.cpp: changes to add static analysis
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src/common/Interval6.cpp: changes to add static analysis
andrewdavidsmith
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src/common/LevelsCounter.cpp: changes to add static analysis
andrewdavidsmith
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src/common/LevelsCounter.hpp: changes to add static analysis
andrewdavidsmith
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src/common/MSite.cpp: changes to add static analysis
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src/common/MSite.hpp: changes to add static analysis
andrewdavidsmith
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src/common/Smoothing.cpp: changes to add static analysis
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src/common/ThreeStateHMM.cpp: changes to add static analysis
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src/common/ThreeStateHMM.hpp: changes to add static analysis
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src/common/TwoStateHMM.cpp: changes to add static analysis
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src/common/TwoStateHMM.hpp: changes to add static analysis
andrewdavidsmith
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src/common/TwoStateHMM_PMD.cpp: changes to add static analysis
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src/common/TwoStateHMM_PMD.hpp: changes to add static analysis
andrewdavidsmith
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src/common/bam_record_utils.cpp: changes to add static analysis
andrewdavidsmith
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src/common/bam_record_utils.hpp: changes to add static analysis
andrewdavidsmith
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src/common/bsutils.cpp: changes to add static analysis
andrewdavidsmith
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src/common/bsutils.hpp: changes to add static analysis
andrewdavidsmith
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src/common/counts_header.cpp: changes to add static analysis
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src/common/counts_header.hpp: changes to add static analysis
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src/common/dnmt_error.hpp: changes to add static analysis
andrewdavidsmith
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src/common/dnmtools_gaussinv.cpp: changes to add static analysis
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src/common/dnmtools_utils.cpp: changes to add static analysis
andrewdavidsmith
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src/common/dnmtools_utils.hpp: changes to add static analysis
andrewdavidsmith
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src/common/numerical_utils.cpp: changes to add static analysis
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src/common/numerical_utils.hpp: changes to add static analysis
andrewdavidsmith
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src/common/xcounts_utils.cpp: changes to add static analysis
andrewdavidsmith
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src/common/xcounts_utils.hpp: changes to add static analysis
andrewdavidsmith
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src/radmeth/dmr.cpp: changes to add static analysis
andrewdavidsmith
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src/radmeth/methdiff.cpp: changes to add static analysis
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src/radmeth/radmeth-adjust.cpp: changes to add static analysis
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src/radmeth/radmeth-merge.cpp: changes to add static analysis
andrewdavidsmith
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src/radmeth/radmeth.cpp: changes to add static analysis
andrewdavidsmith
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src/radmeth/radmeth_design.cpp: changes to add static analysis
andrewdavidsmith
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src/radmeth/radmeth_design.hpp: changes to add static analysis
andrewdavidsmith
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src/radmeth/radmeth_nano.cpp: changes to add static analysis
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src/radmeth/radmeth_optimize_gamma.cpp: changes to add static analysis
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src/radmeth/radmeth_optimize_series.cpp: changes to add static analysis
andrewdavidsmith
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src/radmeth/radmeth_utils.cpp: changes to add static analysis
andrewdavidsmith
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src/radmeth/radmeth_utils.hpp: changes to add static analysis
andrewdavidsmith
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src/utils/clean-hairpins.cpp: changes to add static analysis
andrewdavidsmith
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src/utils/covered.cpp: changes to add static analysis
andrewdavidsmith
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src/utils/fast-liftover.cpp: changes to add static analysis
andrewdavidsmith
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src/utils/format-reads.cpp: changes to add static analysis
andrewdavidsmith
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src/utils/guessprotocol.cpp: changes to add static analysis
andrewdavidsmith
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src/utils/kmersites.cpp: changes to add static analysis
andrewdavidsmith
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src/utils/lc-approx.cpp: changes to add static analysis
andrewdavidsmith
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src/utils/lift-filter.cpp: changes to add static analysis
andrewdavidsmith
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src/utils/merge-bsrate.cpp: changes to add static analysis
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src/utils/merge-methcounts.cpp: changes to add static analysis
andrewdavidsmith
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src/utils/recovered.cpp: changes to add static analysis
andrewdavidsmith
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src/utils/selectsites.cpp: changes to add static analysis
andrewdavidsmith
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src/utils/symmetric-cpgs.cpp: changes to add static analysis
andrewdavidsmith
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src/utils/uniq.cpp: changes to add static analysis
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src/utils/unxcounts.cpp: changes to add static analysis
andrewdavidsmith
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src/utils/xcounts.cpp: changes to add static analysis
andrewdavidsmith
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adding static analysis config files
andrewdavidsmith
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cmake/FindHTSLIB.cmake cmake/static_analysis.cmake: adding the cmake files for htslib and static analysis
andrewdavidsmith
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cmake/static_analysis.cmake: removing the hints for iwyu
andrewdavidsmith
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src/amrfinder/CMakeLists.txt: adding this cmake
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src/amrfinder/allelicmeth.cpp: linting
andrewdavidsmith
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src/common/EpireadStats.hpp: adding a size function for std::size()
andrewdavidsmith
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src/amrfinder/amrfinder.cpp: linting
andrewdavidsmith
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src/amrfinder/amrtester.cpp: linting
andrewdavidsmith
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Adding CMakeLists.txt files
andrewdavidsmith
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data/config.h.in: adding file
andrewdavidsmith
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src/amrfinder/amrfinder.cpp: more linting
andrewdavidsmith
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src/amrfinder/amrtester.cpp: more linting
andrewdavidsmith
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src/mlml/CMakeLists.txt: adding
andrewdavidsmith
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src/common/CMakeLists.txt: adding GSL dependency in cmake
andrewdavidsmith
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src/CMakeLists.txt: Adding all the deps dnmtools binary
andrewdavidsmith
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src/mlml/mlml.cpp: linting
andrewdavidsmith
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src/mlml/mlml.cpp: more linting
andrewdavidsmith
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src/dnmtools.cpp: more linting
andrewdavidsmith
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src/amrfinder/amrfinder.cpp: removing dead code
andrewdavidsmith
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src/common/EpireadStats.cpp: removing commented deadcode
andrewdavidsmith
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src/radmeth/radmeth_design.cpp: removing commented deadcode
andrewdavidsmith
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src/utils/merge-methcounts.cpp: removing commented deadcode
andrewdavidsmith
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src/radmeth/CMakeLists.txt: removing commented deadcode
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src/analysis/pmd.cpp: removing commented deadcode
andrewdavidsmith
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src/common/EpireadStats.cpp: fixing bug with log_likelihood function signature
andrewdavidsmith
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