Using mod functions from htslib - #323

Merged

andrewdavidsmith merged 38 commits into

adding-htslib-mods

Dec 16, 2025

Commits on Nov 29, 2025

src/abismal: Updating submodule
andrewdavidsmith
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aa2e7d2
src/CMakeLists.txt: replacing all individual 'objects' with libraries made to gather objects in each of the subdirs
andrewdavidsmith
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209e01b
src/utils/CMakeLists.txt src/radmeth/CMakeLists.txt src/mlml/CMakeLists.txt src/analysis/CMakeLists.txt src/amrfinder/CMakeLists.txt: adding uniform structure to make a librarry for each subdir's o…
andrewdavidsmith
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a3d9b6c
src/common/nlohmann/json.hpp: adding the nlohmann json lib
andrewdavidsmith
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2363a6d
data/LICENSE: adding the nlohmann json lib
andrewdavidsmith
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806edec
configure.ac: adding version check for htslib
andrewdavidsmith
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7a7a36f
src/analysis/nanopore.cpp: moving to using the htslib functions for modifications in nanopore bams
andrewdavidsmith
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5d6619f
cmake/FindHTSLIB.cmake: fixing the way version numbers are parsed to avoid leading zeros in the major.minor.patch
andrewdavidsmith
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1dfc8d0
multiple CMakeLists.txt: moving the find_package for htslib to the src CMakeLists.txt because the version matters and otherwise it would get confusing
andrewdavidsmith
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ea55710
multiple CMakeLists.txt: moving the find_package for htslib to the src CMakeLists.txt because the version matters and otherwise it would get confusing
andrewdavidsmith
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cdfc313
src/CMakeLists.txt: ensuring threads are obtained
andrewdavidsmith
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42b5919

Commits on Dec 1, 2025

Commits on Dec 2, 2025

Commits on Dec 3, 2025

Commits on Dec 4, 2025

Commits on Dec 5, 2025

Commits on Dec 15, 2025

src/analysis/nanopore.cpp src/dnmtools.cpp src/CMakeLists.txt configure.ac and Makefile.am: adding condition to build for nanopore if htslib version is recent enough to support mods and user reques…
andrewdavidsmith
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41efc92