OBIKmers/obikmer
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  • fe0832190b Merge pull request 'feat(obiread): add static bzip2 and lzma compression support' (#3) from push-qpvrrxpnqlkw into main coissac 2026-05-22 08:29:42 +00:00
  • 72d054c06b feat(obiread): add static bzip2 and lzma compression support Eric Coissac 2026-05-22 10:27:46 +02:00
  • 3d58a32613 Merge pull request 'feat: introduce genome metadata tracking and CSV export' (#2) from push-zrlrptrsrlkk into main coissac 2026-05-22 07:36:11 +00:00
  • 0f8f61d3dd feat: introduce genome metadata tracking and CSV export Eric Coissac 2026-05-22 09:28:58 +02:00
  • 77a0186fae Merge pull request 'Push qkpyqurltlpk' (#1) from push-qkpyqurltlpk into main coissac 2026-05-21 16:57:19 +00:00
  • 13599dd444 feat: Implement query subcommand for sequence-to-genome mapping Eric Coissac 2026-05-21 13:23:05 +02:00
  • c8e591fc78 feat: add superkmer CLI setup and partition bit handling Eric Coissac 2026-05-21 12:17:32 +02:00
  • d9aa211b8f feat: add k-mer index rebuild and compaction feature Eric Coissac 2026-05-21 12:11:55 +02:00
  • 3fa1dbf8cc feat: add pairwise distance computation and phylogenetic trees Eric Coissac 2026-05-21 11:47:35 +02:00
  • 9e1d6f2f25 feat: implement partition-based merge command for k-mer indices Eric Coissac 2026-05-21 11:16:00 +02:00
  • 11182005a2 feat: enhance merge label resolution, debug dump, and layer metadata Eric Coissac 2026-05-21 08:12:02 +02:00
  • 1a1f95e59d feat: add CLI command to export indexed k-mers to CSV Eric Coissac 2026-05-21 06:02:27 +02:00
  • e1d59fde54 feat: add merge command to consolidate k-mer indexes Eric Coissac 2026-05-21 05:53:55 +02:00
  • bfa436ad15 feat: add merge operation specs and partition progress bar Eric Coissac 2026-05-20 21:18:19 +02:00
  • 7d1b62ddf3 refactor: replace single spectrum file with per-partition outputs Eric Coissac 2026-05-20 21:06:27 +02:00
  • c5bcb7b8fa feat: introduce layered MPHF indexing and partition metadata Eric Coissac 2026-05-20 21:01:16 +02:00
  • 17c9e076bd refactor: extract obikindex crate and remove deprecated CLI commands Eric Coissac 2026-05-20 18:21:05 +02:00
  • f8cfb493b8 refactor: extract pipeline stages and centralize partition directory paths Eric Coissac 2026-05-20 15:45:50 +02:00
  • cc2ed4bd31 feat: Add progress tracking and timing instrumentation to index Eric Coissac 2026-05-20 15:02:58 +02:00
  • e66c4d81ef feat(obikmer): add index subcommand for kmer counting pipeline Eric Coissac 2026-05-20 14:37:30 +02:00
  • c20a1ed465 perf: optimize k-mer pipeline with compile-time tables Eric Coissac 2026-05-20 12:37:25 +02:00
  • 9a1c0c0ee0 Add CLI progress bars and throughput metrics to partitioning Eric Coissac 2026-05-19 12:18:12 +02:00
  • b80ab77d66 perf: Switch to sequential PHF construction to avoid thread contention Eric Coissac 2026-05-19 11:49:46 +02:00
  • 6e2a4c977b fix: Replace unreliable memory pressure check with swap indicator Eric Coissac 2026-05-19 11:35:25 +02:00
  • 8c16b79983 feat(obikmer): add obisys profiling to partition pipeline Eric Coissac 2026-05-17 16:01:49 +08:00
  • d0c277d5b6 feat(obisys): Add stage-based performance profiler Eric Coissac 2026-05-17 15:36:20 +08:00
  • 4736a7b6de refactor: restructure k-mer partitioning pipeline for memory efficiency Eric Coissac 2026-05-17 15:34:44 +08:00
  • f36b095ce2 docs: clarify MPHF indexing, storage layout, and distance traits Eric Coissac 2026-05-17 10:20:22 +08:00
  • cf693f17f2 refactor: delegate MPHF construction and I/O to MphfLayer Eric Coissac 2026-05-16 19:30:31 +08:00
  • 13e69e23c9 feat: introduce trait-based distance aggregation and layered store Eric Coissac 2026-05-15 21:18:16 +08:00
  • 45d49ed501 docs: document k-mer index architecture and refactor distance metrics Eric Coissac 2026-05-15 21:07:23 +08:00
  • 8409c852ef feat: Add parallel column counts and partial distance metrics Eric Coissac 2026-05-15 20:41:51 +08:00
  • 8bee9f3017 feat: add parallel distance matrix computation for bit and int matrices Eric Coissac 2026-05-15 17:18:02 +08:00
  • 1881e98bad feat(bitvec): add partial Jaccard, fix padding, optimize constructor Eric Coissac 2026-05-14 21:28:25 +08:00
  • b218bf012b feat: introduce column-major matrix storage and migrate layered map Eric Coissac 2026-05-14 09:31:11 +08:00
  • f48f7500cd refactor(obilayeredmap): support generic payload types Eric Coissac 2026-05-14 09:24:25 +08:00
  • 0b3fcf3cf0 feat: add PersistentBitVec and upgrade PersistentCompactIntVec format Eric Coissac 2026-05-13 21:39:08 +08:00
  • c18c5d2600 feat: add sum and sumadd methods to PersistentCompactIntVec Eric Coissac 2026-05-13 10:51:23 +08:00
  • 0733287de5 feat(obicompactvec): migrate to memory-mapped file storage Eric Coissac 2026-05-13 10:47:39 +08:00
  • dfce956162 feat(obicompactvec): implement Iterator for PersistentCompactIntVec Eric Coissac 2026-05-13 10:25:14 +08:00
  • 4d5fcd4340 refactor: split obicompactvec storage into primary and overflow files Eric Coissac 2026-05-13 10:20:15 +08:00
  • f2de79acde Add persistent compact integer vector and cache-line-optimized MPHF Eric Coissac 2026-05-13 06:24:43 +08:00
  • 84ed752b78 perf: optimize packed_seq sub() with direct bit-slice copying Eric Coissac 2026-05-12 22:30:45 +08:00
  • ff75c9198d feat: add kmer iterators and optimize layered map performance Eric Coissac 2026-05-12 22:28:01 +08:00
  • 9c41891cc8 feat: add obilayeredmap crate for disk-backed k-mer indexing Eric Coissac 2026-05-12 14:05:18 +08:00
  • 962e386f8b docs: clarify iterator borrowing vs consuming semantics Eric Coissac 2026-05-11 11:40:44 +08:00
  • 7bc9aa9af5 refactor(packed_seq): unify kmer iterators with generic storage Eric Coissac 2026-05-11 11:13:30 +08:00
  • 6687911d60 Add consuming k-mer iterators to PackedSeq and Superkmer Eric Coissac 2026-05-11 10:21:35 +08:00
  • 92cda13ae4 refactor: streamline I/O handling and remove deprecated codec module Eric Coissac 2026-05-09 19:19:33 +08:00
  • 9e5af6b5a5 refactor(pool): optimize write batch and LRU cache handling Eric Coissac 2026-05-09 18:58:53 +08:00
  • e008a8beb4 harden obiskio error handling with explicit variants and bounds checking Eric Coissac 2026-05-09 18:26:08 +08:00
  • 5169f65dc9 feat: implement persistent layered index and chunked binary format Eric Coissac 2026-05-09 17:20:08 +08:00
  • 8c17bf958b refactor: centralize k-mer config and introduce packed sequences Eric Coissac 2026-05-05 18:08:19 +02:00
  • 602f414957 fix: strip AI reasoning blocks from commit messages Eric Coissac 2026-05-02 18:01:31 +02:00
  • 0b784242cf refactor: split traversal logic in start_iter for clearer chain/cycle handling Eric Coissac 2026-05-02 16:28:44 +02:00
  • 86e9cb7026 refactor: improve de Bruijn graph traversal and longtig generation Eric Coissac 2026-05-01 23:05:21 +02:00
  • 35840b9d73 refactor: simplify unitig iteration logic and API Eric Coissac 2026-05-01 13:52:13 +02:00
  • defeeb9460 feat: enforce canonical k-mer representation throughout the codebase Eric Coissac 2026-05-01 13:34:55 +02:00
  • 21ddbf1674 feat: add seq_hash() and refactor canonical hashing Eric Coissac 2026-05-01 10:35:17 +02:00
  • 27f5e88a7b refactor: implement RoutableSuperKmer and update k-mer indexing pipeline Eric Coissac 2026-04-29 22:52:42 +02:00
  • 4e26e3bd40 Refactor: Simplify user authentication flow Eric Coissac 2026-04-29 08:45:49 +02:00
  • 97e65bd831 ♻️ refactor pipeline architecture and fix macOS memory detection Eric Coissac 2026-04-28 08:40:07 +02:00
  • 4c19882f03 ✨ add PhantomData import for generic type safety Eric Coissac 2026-04-27 23:27:42 +02:00
  • ebbfe35cbc Refactor: Extract utility function for string reversal Eric Coissac 2026-04-27 20:23:44 +02:00
  • e7fa60a3a2 Refactor: Simplify user authentication flow Eric Coissac 2026-04-27 20:17:06 +02:00
  • 58391886a3 🔧 Replace degenerate minimizer logic with hash-based random ordering Eric Coissac 2026-04-27 16:56:13 +02:00
  • 7efec54b27 .gitignore: ignore zstandard-compressed files Eric Coissac 2026-04-27 16:53:42 +02:00
  • 1f466bf113 Refactor: simplify user authentication flow Eric Coissac 2026-04-26 14:59:07 +02:00
  • eaf893174f ♻️ refactor(obikpartitionner): replace low-level I/O with obiskio::SKFileWriter Eric Coissac 2026-04-26 14:58:41 +02:00
  • c09d17401d + obiskio: add binary I/O with LRU pool and compression Eric Coissac 2026-04-24 21:07:58 +02:00
  • d4e4289aff (feat): refactor superkmer to use obipipeline with flat transforms Eric Coissac 2026-04-24 18:16:47 +02:00
  • f1c8fc85c9 ⬆️ refactor superkmer to use obipipeline Eric Coissac 2026-04-24 18:14:00 +02:00
  • 75bf980046 (deps) Add regex crate and improve MIME type detection Eric Coissac 2026-04-24 17:14:33 +02:00
  • 22951fb0e8 🔖 Add obipipeline parallel pipeline library Eric Coissac 2026-04-24 08:52:46 +02:00
  • 3f8880a7e5 📦 Add infer and new pipeline infrastructure Eric Coissac 2026-04-23 21:03:48 +02:00
  • 664d0216b5 📦 Add obipipeline crate and refactor path handling Eric Coissac 2026-04-20 20:02:58 +02:00
  • 380b5a6f94 📖 Update super-kmer theory and implementation to prefer non-degenerate m-mers Eric Coissac 2026-04-20 17:49:52 +02:00
  • b534c693ac 🔧 refactor(iter): simplify minimizer access via new canonical_minimizer_raw() Eric Coissac 2026-04-20 16:57:50 +02:00
  • 5e77ea4eba 🗑️ Refactor entropy and minimizer logic into RollingStat Eric Coissac 2026-04-20 16:44:00 +02:00
  • b4accf1149 [obiskbuilder] Add canonical k-mer tables and refactor entropy computation Eric Coissac 2026-04-20 15:56:17 +02:00
  • f09b70b209 🔧 Fix rolling k-mer and minimizer logic Eric Coissac 2026-04-20 15:43:44 +02:00
  • ae5e1152b9 (feat) Add entropy-based filtering and rolling statistics for k-mers Eric Coissac 2026-04-20 15:34:56 +02:00
  • 097f7f0695 🔧 refactor cursor API and normalize chunking logic Eric Coissac 2026-04-19 22:47:26 +02:00
  • 3716eeff7f ✨ Add offset-based sub-cursors and Rope seek mode Eric Coissac 2026-04-19 22:10:19 +02:00
  • 41095a40d0 Refactor: simplify logic and fix edge case Eric Coissac 2026-04-19 21:31:16 +02:00
  • 2429131851 Refactor: Simplify user authentication flow Eric Coissac 2026-04-19 21:30:04 +02:00
  • 0dcb5dd6c2 ♻️ refactor rope implementation to use obikrope Eric Coissac 2026-04-19 21:22:10 +02:00
  • 5fab59f92c Add target to .gitignore Eric Coissac 2026-04-19 15:56:16 +02:00
  • de3f9b16cf first implementation but far to be optimal Eric Coissac 2026-04-16 22:38:20 +02:00