Reduced dependency on smithlab_cpp#98

Merged

andrewdavidsmith merged 10 commits intomasterfrom

reduced-dependency-on-smithlab-cpp

Dec 23, 2025

Commits on Dec 23, 2025

src/AbismalIndex.cpp: making the static analysis exceptions specific
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src/abismal.cpp: some refactoring and adding option to output JSON for the summary stats
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data/LICENSE: updating for JSON
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src/nlohmann/json.hpp: adding json lib
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data/LICENSES.inc.in: adding a template for a header for license info
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data/md5sum.txt: updating the hashes to reflect a bugfix when updating end2_stats which was assuming end2 had the same length as end1
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src/abismal.cpp: fixing very recent bug that swapped the isize in end2 output for paired-end
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src/common.hpp: adding this source
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src/common.hpp and src/abismal.cpp: fixing missing include info
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Makefile.am: adding json to dist
andrewdavidsmith
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