Using mod functions from htslib#323

Merged

andrewdavidsmith merged 38 commits intomasterfrom

adding-htslib-mods

Dec 16, 2025

Commits on Nov 29, 2025

src/abismal: Updating submodule
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src/CMakeLists.txt: replacing all individual 'objects' with libraries made to gather objects in each of the subdirs
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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…
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src/common/nlohmann/json.hpp: adding the nlohmann json lib
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data/LICENSE: adding the nlohmann json lib
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configure.ac: adding version check for htslib
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src/analysis/nanopore.cpp: moving to using the htslib functions for modifications in nanopore bams
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cmake/FindHTSLIB.cmake: fixing the way version numbers are parsed to avoid leading zeros in the major.minor.patch
andrewdavidsmith
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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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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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src/CMakeLists.txt: ensuring threads are obtained
andrewdavidsmith
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Commits on Dec 1, 2025

Commits on Dec 2, 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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