Upgrade sshash to v5.0.0 with API compatibility changes#594
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adamant-pwn wants to merge 3 commits intomasterfrom
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Upgrade sshash to v5.0.0 with API compatibility changes#594adamant-pwn wants to merge 3 commits intomasterfrom
adamant-pwn wants to merge 3 commits intomasterfrom
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Upgraded sshash from previous version to v5.0.0 (upstream master). This required significant API adaptation due to breaking changes. API changes handled: 1. dictionary now requires two template parameters: dictionary<Kmer, Offsets> - Added sshash::decoded_offsets as second parameter throughout 2. Method renames: - size() → num_kmers() - lookup_advanced() → lookup() 3. streaming_query template parameter changed: - Was: streaming_query<kmer_t, bool> - Now: streaming_query<Dict, bool> (takes dictionary type) 4. Use dictionary::kmer_type instead of template_parameter extraction - Replaced get_kmer_t helper with decltype(dict)::kmer_type - Cleaner approach using built-in typedef from sshash Code quality improvements: - Removed template_parameter helper struct and get_kmer_t alias - Simplified kmer type extraction in lambda expressions Submodule update: - Updated external-libraries/sshash to merge-upstream-master-with-metagraph-compatibility - Includes cityhash namespace wrapping and accessor methods - Includes pthash fix for multiple definition errors
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Updates: 1. Bump sshash submodule to include: - Fix for sparse index bit budget calculation - Conditional verbose output (respects build_config.verbose) 2. Clean integration with sshash verbose flag: - Set build_config.verbose = common::get_verbose() - Remove stdout/stderr disabling hack (no longer needed) - Library now respects its own configuration This completes the sshash v5.0.0 integration with all bug fixes. All 150 DBGSSHash tests passing.
- Track only buckets with size > 1 for sparse index encoding - Renamed m_max_buckets_per_size to m_max_sparse_buckets_per_size - Size-1 buckets use direct offset encoding
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Upgraded sshash from previous version to v5.0.0 (upstream master). This required significant API adaptation due to breaking changes.
API changes handled:
dictionary now requires two template parameters: dictionary<Kmer, Offsets>
Method renames:
streaming_query template parameter changed:
Use dictionary::kmer_type instead of template_parameter extraction
Code quality improvements:
Submodule update: