OBIKmers/obikmer
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  • 0f389b37f2 Merge pull request 'chore: bump obikmer to 1.2.1 and disable obikindex default features' (#69) from push-vzoxtyuuuxqn into main main coissac 2026-08-17 11:33:56 +00:00
  • 66ab1d0947 chore: bump obikmer to 1.2.1 and disable obikindex default features v1.2.2 Eric Coissac 2026-08-17 13:30:16 +02:00
  • 5e2bb393e0 Merge pull request 'Push luqxvxskktxv' (#68) from push-luqxvxskktxv into main coissac 2026-08-17 10:35:12 +00:00
  • fceb523f1a chore: disable default features for obikindex v1.2.1 Eric Coissac 2026-08-17 12:31:40 +02:00
  • 700eaeaed2 test: simplify k-mer test setup for updated canonical API Eric Coissac 2026-08-17 12:25:56 +02:00
  • f1f7940277 Merge pull request 'Push zpwxxpnpktps' (#67) from push-zpwxxpnpktps into main coissac 2026-08-17 09:41:41 +00:00
  • 6def18fa88 Add TNT configuration directives and tree export commands to script v1.2.0 Eric Coissac 2026-08-16 20:41:04 +02:00
  • 70b0527957 Add diagnostic logging and minor internal refactoring Eric Coissac 2026-08-16 15:15:43 +02:00
  • 11476bc557 Add sparse bit matrix support and enhance dimension logging Eric Coissac 2026-08-16 13:05:27 +02:00
  • dbb969f087 style: reformat iqtree module for line-length compliance Eric Coissac 2026-08-16 11:36:05 +02:00
  • 1f9c6388eb Introduce compare_sparse CLI tool to verify index consistency Eric Coissac 2026-08-16 09:22:41 +02:00
  • 128db64564 feat(phylo): add --iqtree-min-freq to filter rare nucleotide states Eric Coissac 2026-08-15 22:38:40 +02:00
  • c8f2b16b4c fix: prevent probability underflow in pairwise cost matrix Eric Coissac 2026-08-15 21:46:22 +02:00
  • 9654201885 feat: introduce _iqtree_states.csv for compact symbol mapping Eric Coissac 2026-08-15 21:30:54 +02:00
  • c6cfdac043 perf: optimize entropy computation by pre-filtering monomorphic minorants Eric Coissac 2026-08-15 21:16:04 +02:00
  • 7bac0f3850 large refactoring Eric Coissac 2026-08-15 20:56:29 +02:00
  • 49e66f16a2 docs: document architecture analysis and refactoring plans for siblings Eric Coissac 2026-08-15 20:15:43 +02:00
  • 53c40b7a53 refactor: format tnt script generation and add tree export commands Eric Coissac 2026-08-15 19:45:08 +02:00
  • 3ba26b3dc1 feat: add sparse on-disk format for presence matrices Eric Coissac 2026-08-15 19:19:48 +02:00
  • 50f4820cb9 feat(obicompactvec): introduce sparse bit matrix with supporting primitives Eric Coissac 2026-08-15 15:59:03 +02:00
  • 45b19503a1 Add proportional subsampling and Shannon entropy calculation Eric Coissac 2026-08-15 09:50:02 +02:00
  • f5e4bbfc6b Document architecture redesign and add partition layer accessor Eric Coissac 2026-08-14 22:45:08 +02:00
  • 151493526c perf: add #[inline] attributes to obicompactvec methods Eric Coissac 2026-08-14 22:29:46 +02:00
  • 693c18bfa7 introduce fast mode for optimized sibling presence checks Eric Coissac 2026-08-14 21:29:38 +02:00
  • 0ce934b111 Refactor sibling annex to use mmap-backed concurrent storage Eric Coissac 2026-08-14 21:02:51 +02:00
  • fecfe84ea6 Move sibling annex implementation to obikphylo siblings module Eric Coissac 2026-08-14 20:27:35 +02:00
  • c990087ef3 Add execution timing and parallelize sibling stats Eric Coissac 2026-08-14 18:55:48 +02:00
  • 32d6720f50 Fix batch enumeration offsets and refactor sibling annex construction Eric Coissac 2026-08-14 17:23:59 +02:00
  • d2548e8c33 feat(progress): implement configurable ETA throttling Eric Coissac 2026-08-14 15:52:31 +02:00
  • 5997de6707 Extract phylogenetic sibling logic into new obikphylo crate Eric Coissac 2026-08-14 13:53:05 +02:00
  • 519195d4a1 Replace slot-based indexing with iteration order and stream k-mers Eric Coissac 2026-08-14 13:18:43 +02:00
  • b1f54b7d2f Add cache-optimized batch retrieval and sub-matrix methods Eric Coissac 2026-08-14 12:06:35 +02:00
  • dae543fdfc Add raw lookup and iteration APIs to Layer struct Eric Coissac 2026-08-14 11:05:11 +02:00
  • 0de078fdf1 Store minorant flag in family mask to avoid costly k-mer reconstruction Eric Coissac 2026-08-14 10:06:44 +02:00
  • c7679fac90 refactor: replace eager family collection with callback processing Eric Coissac 2026-08-14 08:26:45 +02:00
  • 0e2e3b5bae Switch sibling modules to sequential layer directory processing Eric Coissac 2026-08-14 08:08:45 +02:00
  • cd57cf0cbd refactor: extract sibling family scanning into shared module Eric Coissac 2026-08-14 07:50:39 +02:00
  • 3da501349b docs: clarify phylogenetic output files and tool usage Eric Coissac 2026-08-14 07:43:07 +02:00
  • d54ae272a4 refactor: centralize index setup logic and add progress bar ETA Eric Coissac 2026-08-13 22:55:49 +02:00
  • eee71430a4 add name-tree command and fix --free-loss cost matrix Eric Coissac 2026-08-13 22:25:08 +02:00
  • 8615da59a8 Add phylogenetic CLI options for family overlap and missing data Eric Coissac 2026-08-13 21:14:35 +02:00
  • e2b9374426 fix: respect --force flag during index and partition creation Eric Coissac 2026-08-13 19:35:40 +02:00
  • dd889854cb rename distance subcommand to phylo Eric Coissac 2026-08-13 16:33:22 +02:00
  • 79346c0c86 Add modular data structures, parallel pipelines, and system profiling Eric Coissac 2026-08-13 12:55:36 +02:00
  • cc67023e2c feat: centralize genome metadata predicates in obikindex Eric Coissac 2026-08-13 10:21:54 +02:00
  • 8967a20ed7 refactor(cmd): restructure modules and decompose query command Eric Coissac 2026-08-13 10:12:00 +02:00
  • 6acafa7f2c docs: add obikmer user guide and MkDocs build configuration Eric Coissac 2026-08-13 10:01:29 +02:00
  • 0c86ea0385 Replace Sankoff cost matrix with cardinality-composition decomposition Eric Coissac 2026-08-13 09:29:44 +02:00
  • c26623fa00 Add repeatable --exclude-genome flag to obikmer distance command Eric Coissac 2026-08-12 19:51:35 +02:00
  • 28d841c7be feat(distance): add IQ-TREE output and optimize state index mapping Eric Coissac 2026-08-12 18:23:51 +02:00
  • adf5b52dc7 feat(distance): implement native Sankoff calibration and backends Eric Coissac 2026-08-12 18:23:22 +02:00
  • 55d7fa2067 feat: add Sankoff parsimony model and directory locking Eric Coissac 2026-08-12 15:27:39 +02:00
  • 14aa82521d Merge pull request 'fix: resolve test race conditions, add logging, and fix CI deadlock' (#66) from push-kywuzlnvrqyx into main coissac 2026-08-11 21:05:09 +00:00
  • c95c47155e fix: resolve test race conditions, add logging, and fix CI deadlock v1.1.44 Eric Coissac 2026-08-11 19:35:54 +02:00
  • 4f6d442688 Merge pull request 'ci: disable numa feature, bump obikmer, and document Sankoff costs' (#65) from push-oruynkvporsn into main coissac 2026-08-11 16:28:07 +00:00
  • e6f0ca472c ci: disable numa feature, bump obikmer, and document Sankoff costs v1.1.43 Eric Coissac 2026-08-11 18:25:26 +02:00
  • 442f7a9e4c Merge pull request 'chore: update ci cache, document distance metrics, and bump version' (#64) from push-wpxsvyylwmsq into main coissac 2026-08-11 15:17:42 +00:00
  • a63692b8c4 chore: update ci cache, document distance metrics, and bump version v1.1.42 Eric Coissac 2026-08-11 15:03:51 +02:00
  • fa82989ea9 Merge pull request 'refactor: centralize CPU core detection using cgroup-aware utility' (#63) from push-lqzukpulzykz into main coissac 2026-08-11 10:35:06 +00:00
  • 5f95e866f8 refactor: centralize CPU core detection using cgroup-aware utility v1.1.41 Eric Coissac 2026-08-11 12:17:26 +02:00
  • 2e7cfc4368 Merge pull request 'Push lsqnpxrxuvpp' (#62) from push-lsqnpxrxuvpp into main coissac 2026-08-11 09:09:23 +00:00
  • f5e508ed33 feat: add multi-genome SNP pseudo-alignment and CLI export v1.1.40 Eric Coissac 2026-08-10 22:12:12 +02:00
  • 49f329edd5 feat: add raw SNP distance calculation and CLI flag Eric Coissac 2026-08-10 17:31:48 +02:00
  • 1a470eab9e Refactor k-mer sibling tracking to compact bitmask and on-demand counts Eric Coissac 2026-08-10 17:21:04 +02:00
  • ba990a48a0 feat: add obipipeline for concurrent sibling annex stats Eric Coissac 2026-08-10 15:27:35 +02:00
  • ea914bb536 feat: implement per-k-mer sibling counts and central neighbor generation Eric Coissac 2026-08-10 14:56:44 +02:00
  • 8bc6d533e5 feat: support negative count filters as group size offsets Eric Coissac 2026-08-10 12:35:27 +02:00
  • 45df9919e5 docs: add central-position SNP distance estimator spec Eric Coissac 2026-07-10 09:47:19 +02:00
  • 2610a4af79 feat: add Mash distance metric and rolling entropy support Eric Coissac 2026-07-09 11:37:52 +02:00
  • dc3392865f Merge pull request 'Push qowsvpqmoukq' (#61) from push-qowsvpqmoukq into main coissac 2026-07-08 18:05:42 +00:00
  • fd2c23e7df refactor: remove equivalence class folding from entropy pipeline v1.1.39 Eric Coissac 2026-07-08 19:26:33 +02:00
  • 912f788f7f feat: extract k-mer entropy computation into new obikentropy crate Eric Coissac 2026-07-08 18:16:08 +02:00
  • e725523898 feat: add entropy-driven k-mer complexity filtering Eric Coissac 2026-07-08 12:39:21 +02:00
  • 165982fb07 Merge pull request 'Bump obikmer version to 1.1.38 and add memory footprint logging' (#60) from push-slxmykzqmzzv into main coissac 2026-07-08 10:15:51 +00:00
  • 2740f52326 Bump obikmer version to 1.1.38 and add memory footprint logging v1.1.38 Eric Coissac 2026-07-08 12:11:50 +02:00
  • dff5d2f457 Merge pull request 'Push smluomvxpptv' (#59) from push-smluomvxpptv into main coissac 2026-07-07 17:13:03 +00:00
  • eea884f393 ci: improve release workflow and bump obikmer to v1.1.37 v1.1.37 Eric Coissac 2026-07-07 18:55:12 +02:00
  • ae42a061bd perf: optimize k-mer queries with sparse index and run-based aggregation Eric Coissac 2026-07-07 18:51:56 +02:00
  • 040eff140c refactor(query): optimize mmap locality with column-major matrix fetch Eric Coissac 2026-07-07 18:36:25 +02:00
  • a348637f3b refactor(query): deduplicate k-mers upfront and split MPHF lookup Eric Coissac 2026-07-07 16:14:10 +02:00
  • 9d7ced4493 perf(query): replace static divisor with dynamic overhead multiplier Eric Coissac 2026-07-07 16:11:19 +02:00
  • 9d49929b0c refactor(query): implement throttled per-file streaming pipeline Eric Coissac 2026-07-07 16:06:32 +02:00
  • 61c390503d feat(query): add throughput metering and --max-open-files flag Eric Coissac 2026-07-07 15:12:09 +02:00
  • 8f0ceec784 docs: clarify query processing and add performance roadmap Eric Coissac 2026-07-07 15:08:50 +02:00
  • 00b4b1fa51 docs: add future work section for parallel gzip decompression Eric Coissac 2026-07-07 13:41:24 +02:00
  • e96ad38c8e Merge pull request 'feat: filter zero-valued entries from kmer strict matches output' (#58) from push-rosnxrytzxzk into main coissac 2026-07-07 09:22:02 +00:00
  • 4fc7860825 feat: filter zero-valued entries from kmer strict matches output v1.1.36 Eric Coissac 2026-07-07 10:47:47 +02:00
  • 5bdc0f826a Merge pull request 'fix: validate packed matrix columns before repacking' (#57) from push-vkqvorvsqnqx into main coissac 2026-07-03 15:26:55 +00:00
  • cd2f2f9417 fix: validate packed matrix columns before repacking v1.1.35 Eric Coissac 2026-07-03 17:16:36 +02:00
  • 7844239a8e Merge pull request 'Push msotyzponsls' (#56) from push-msotyzponsls into main coissac 2026-07-03 11:28:49 +00:00
  • 2b37e8aac4 fix(bitmatrix): explicitly compute diagonal entries for self-similarity v1.1.34 Eric Coissac 2026-07-03 13:01:39 +02:00
  • 67b4e4da53 refactor(numa): replace flat runner with per-node activation channels Eric Coissac 2026-07-03 12:47:56 +02:00
  • 66ab4c6db1 Merge pull request 'feat(numa): introduce I/O sampling to prevent activation stalls' (#55) from push-ooruxnkktvvz into main coissac 2026-07-02 09:36:19 +00:00
  • f84dd539bf feat(numa): introduce I/O sampling to prevent activation stalls v1.1.33 Eric Coissac 2026-07-02 10:05:31 +02:00
  • 6378734e1c Merge pull request 'fix(obisys): remove activation guard to always update metrics' (#54) from push-vkloynurrxzu into main coissac 2026-07-01 18:34:10 +00:00
  • b3a617cce1 fix(obisys): remove activation guard to always update metrics v1.1.32 Eric Coissac 2026-07-01 19:49:23 +02:00
  • 2080e5e8a9 Merge pull request 'ci: fix registry auth and bump obikmer to 1.1.30' (#53) from push-zxlknspoxknt into main coissac 2026-07-01 14:20:09 +00:00
  • 45ed2bc9b8 ci: fix registry auth and bump obikmer to 1.1.30 v1.1.30 Eric Coissac 2026-07-01 14:30:23 +02:00
  • aa126fd89d Merge pull request 'feat: simplify worker spawning logic and update macOS build workflow' (#52) from push-uvmlknmzqqnx into main coissac 2026-07-01 09:50:51 +00:00
  • c612132763 feat: simplify worker spawning logic and update macOS build workflow v1.1.29 Eric Coissac 2026-07-01 11:35:06 +02:00