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Diff for: libs/genesis
- .github/workflows/ci.yaml+46-7
- CMakeLists.txt+21-10
- lib/genesis/placement/simulator/distributions.cpp+9-2
- lib/genesis/population/function/fst_pool_functions.hpp+9-8
- lib/genesis/population/function/genome_locus.hpp+4-3
- lib/genesis/sequence/formats/fastq_writer.cpp+3-2
- lib/genesis/sequence/formats/fastq_writer.hpp+4-4
- lib/genesis/sequence/formats/fastx_input_view_stream.hpp+4-3
- lib/genesis/sequence/formats/fastx_output_stream.hpp+6-6
- lib/genesis/sequence/kmer/bitfield.hpp+3-2
- lib/genesis/sequence/kmer/canonical_encoding.cpp+46
- lib/genesis/sequence/kmer/canonical_encoding.hpp+42-43
- lib/genesis/sequence/kmer/extractor.hpp+84-43
- lib/genesis/sequence/kmer/function.hpp+38-50
- lib/genesis/sequence/kmer/kmer.hpp+22-64
- lib/genesis/sequence/kmer/microvariant_scanner.hpp+15-19
- lib/genesis/taxonomy/accession_lookup.hpp+267
- lib/genesis/taxonomy/formats/accession_lookup_reader.hpp+356
- lib/genesis/taxonomy/formats/ncbi.cpp+174-58
- lib/genesis/taxonomy/formats/ncbi.hpp+82-22
- lib/genesis/taxonomy/formats/taxonomy_reader.cpp+7-5
- lib/genesis/taxonomy/formats/taxopath_generator.cpp+5-5
- lib/genesis/taxonomy/functions/taxonomy.cpp+19-7
- lib/genesis/taxonomy/functions/taxonomy.hpp+11-10
- lib/genesis/taxonomy/printers/nested.cpp+42-12
- lib/genesis/taxonomy/printers/nested.hpp+17-7
- lib/genesis/taxonomy/taxon.cpp-224
- lib/genesis/taxonomy/taxon.hpp+157-67
- lib/genesis/taxonomy/taxonomy.cpp+76-208
- lib/genesis/taxonomy/taxonomy.hpp+186-64
- lib/genesis/utils.hpp+1
- lib/genesis/utils/containers/function_cache.hpp+8-4
- lib/genesis/utils/containers/interval_tree/functions.hpp+7-6
- lib/genesis/utils/containers/interval_tree/interval.hpp+17-4
- lib/genesis/utils/containers/optional.hpp+10-15
- lib/genesis/utils/containers/transform_iterator.hpp+7-6
- lib/genesis/utils/core/info.cpp+8-5
- lib/genesis/utils/core/info.hpp+2-2
- lib/genesis/utils/core/std.hpp+109
- lib/genesis/utils/formats/csv/input_iterator.hpp+19-4
- lib/genesis/utils/formats/json/document.hpp+19-9
- lib/genesis/utils/formats/json/iterator.hpp+2-2
- lib/genesis/utils/io/input_stream.cpp+3-2
- lib/genesis/utils/io/input_stream.hpp+5-4
- lib/genesis/utils/io/parser.cpp+16-10
- lib/genesis/utils/threading/concurrent_vector_guard.hpp+239
- lib/genesis/utils/threading/thread_functions.hpp+3-1
- lib/genesis/utils/threading/thread_pool.hpp+13-4
- test/src/sequence/kmer.cpp+81-78
- test/src/utils/threading/concurrent_vector_guard.cpp+91
- tools/cmake/DetectCppVersion.cmake+142
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