Searched refs:SeedEncoding (Results 1 – 11 of 11) sorted by relevance
| /dports/biology/diamond/diamond-2.0.13/src/data/ |
| H A D | seed_histogram.cpp | 48 SeedHistogram::SeedHistogram(Block& seqs, bool serial, const Filter* filter, SeedEncoding code, con… in SeedHistogram()
88 template SeedHistogram::SeedHistogram(Block&, bool, const NoFilter*, SeedEncoding, const std::vecto…
89 template SeedHistogram::SeedHistogram(Block&, bool, const SeedSet*, SeedEncoding, const std::vector…
90 template SeedHistogram::SeedHistogram(Block&, bool, const HashedSeedSet*, SeedEncoding, const std::…
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| H A D | flags.h | 7 enum class SeedEncoding { SPACED_FACTOR, HASHED, CONTIGUOUS }; enum
41 const SeedEncoding code;
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| H A D | seed_array.cpp | 39 static size_t seed_bits(const SeedEncoding code) { in seed_bits()
41 case SeedEncoding::HASHED: in seed_bits()
43 case SeedEncoding::SPACED_FACTOR: in seed_bits()
45 case SeedEncoding::CONTIGUOUS: in seed_bits()
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| H A D | seed_set.cpp | 72 const EnumCfg cfg{ &p, 0, 1, SeedEncoding::CONTIGUOUS, skip, true, false, seed_cut, soft_masking }; in SeedSet()
99 …const EnumCfg cfg{ &p, 0, shapes.count(), SeedEncoding::HASHED, skip, false, false, seed_cut, soft… in HashedSeedSet()
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| H A D | seed_histogram.h | 90 …SeedHistogram(Block& seqs, bool serial, const Filter* filter, SeedEncoding code, const std::vector…
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| H A D | enum_seeds.h | 102 if (cfg->code == SeedEncoding::CONTIGUOUS) { in enum_seeds_worker()
136 else if (cfg->code == SeedEncoding::HASHED) { in enum_seeds_worker()
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| /dports/biology/diamond/diamond-2.0.13/src/run/ |
| H A D | config.h | 34 enum class SeedEncoding; variable
62 SeedEncoding seed_encoding;
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| H A D | config.cpp | 20 seed_encoding(config.target_indexed ? SeedEncoding::HASHED : SeedEncoding::SPACED_FACTOR), in Config()
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| H A D | double_indexed.cpp | 249 options.seed_encoding = SeedEncoding::HASHED; in run_query_iteration()
256 options.seed_encoding = SeedEncoding::CONTIGUOUS; in run_query_iteration()
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| /dports/biology/diamond/diamond-2.0.13/src/search/ |
| H A D | seed_complexity.cpp | 75 if (cfg.seed_encoding != SeedEncoding::SPACED_FACTOR) in mask_seeds()
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| /dports/biology/diamond/diamond-2.0.13/src/tools/ |
| H A D | tools.cpp | 120 …EnumCfg cfg{ &parts, 0, 1, SeedEncoding::SPACED_FACTOR, nullptr, false, false, config.seed_cut_, M… in list_seeds()
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