Commit Graph

Select branches

Hide Pull Requests

main

push-nvvqmzmrotxx

push-vtvurtklymss

#1

#10

#11

#12

#13

#14

#15

#16

#17

#18

#19

#2

#20

#21

#22

#23

#24

#25

#26

#27

#28

#29

#3

#30

#31

#32

#33

#34

#35

#36

#37

#38

#39

#4

#40

#41

#42

#43

#44

#45

#46

#47

#48

#49

#5

#50

#51

#52

#53

#54

#55

#56

#57

#6

#7

#8

#9

v1.1.11

v1.1.12

v1.1.13

v1.1.14

v1.1.15

v1.1.16

v1.1.17

v1.1.18

v1.1.19

v1.1.20

v1.1.21

v1.1.24

v1.1.25

v1.1.26

v1.1.27

v1.1.29

v1.1.30

v1.1.32

v1.1.33

v1.1.34

v1.1.35

v1.1.6

v1.1.7

v1.1.9

Mono Color

• 7208dcbb4a Merge pull request 'refactor: defer SrcLayerData lookups in RawBatch' (#25) from push-nxrynoorswrw into main coissac 2026-06-12 20:19:21 +00:00
• 2e69b0b7fe refactor: defer SrcLayerData lookups in RawBatch Eric Coissac 2026-06-12 22:09:23 +02:00
• 9ea1dff5d6 Merge pull request 'Push rwqsmuvystym' (#24) from push-rwqsmuvystym into main coissac 2026-06-12 19:33:20 +00:00
• b2c8373586 refactor: parallelize merge layer with WorkerPool pipeline Eric Coissac 2026-06-12 21:28:48 +02:00
• ba49af6f9e refactor: parallelize merge and partition logic with obipipeline Eric Coissac 2026-06-12 20:54:44 +02:00
• 2bc189e962 feat: dynamically compute seed expansion based on RSS Eric Coissac 2026-06-12 16:28:03 +02:00
• db9c604199 Merge pull request 'feat: enhance memory budgeting and add rebuild diagnostics' (#23) from push-nptzpkomspkv into main coissac 2026-06-12 13:21:12 +00:00
• 52fd2cf801 feat: enhance memory budgeting and add rebuild diagnostics Eric Coissac 2026-06-12 15:18:37 +02:00
• 97e3fb9761 Merge pull request 'Push ylnwstyzqwrt' (#22) from push-ylnwstyzqwrt into main coissac 2026-06-12 10:10:03 +00:00
• b5e027f23b feat: add memory-aware parallel merge scheduling and CLI flags Eric Coissac 2026-06-12 11:26:24 +02:00
• f44fe042bc feat: add parallel k-mer counting and stats CLI Eric Coissac 2026-06-12 08:49:11 +02:00
• 94e0a370b3 Merge pull request 'Push tmpsxsztwpxl' (#21) from push-tmpsxsztwpxl into main coissac 2026-06-09 13:31:25 +00:00
• 970460be42 refactor: rename rebuild subcommand to filter Eric Coissac 2026-06-09 15:22:57 +02:00
• e66adef23d feat: add select command for genome column projection and aggregation Eric Coissac 2026-06-09 15:05:08 +02:00
• b0dab452f6 Merge pull request 'refactor: optimize dump partition iteration and add progress tracking' (#20) from push-xqswlxlvmyrq into main coissac 2026-06-09 09:34:13 +00:00
• db730e9cf6 refactor: optimize dump partition iteration and add progress tracking Eric Coissac 2026-06-09 11:04:49 +02:00
• f65ecd19cc Merge pull request 'Push lrwmyplxxzkn' (#19) from push-lrwmyplxxzkn into main coissac 2026-06-09 08:28:20 +00:00
• 7dd8db1409 docs: document conservative rounding strategy for filtering thresholds Eric Coissac 2026-06-09 10:24:25 +02:00
• ce45e2fbe1 refactor: centralize k-mer filtering logic and add validation Eric Coissac 2026-06-09 09:57:38 +02:00
• 2465cfbc4b Parallelize partition iteration using Rayon Eric Coissac 2026-06-09 09:54:41 +02:00
• d626d42ec7 feat: add --head and --presence-threshold to dump and distance Eric Coissac 2026-06-09 09:47:44 +02:00
• 650eea43b6 Merge pull request 'Push quqlpklvxsqx' (#18) from push-quqlpklvxsqx into main coissac 2026-06-08 18:15:01 +00:00
• eb7805c747 feat: add configurable presence threshold to kmer distance Eric Coissac 2026-06-08 20:13:07 +02:00
• 1ec65922df feat: implement parallel pairwise distance matrices Eric Coissac 2026-06-08 20:04:51 +02:00
• 09d9e21744 feat: integrate tracing and enhance bit matrix operations Eric Coissac 2026-06-08 19:48:17 +02:00
• 3f47e22083 Merge pull request 'Push pvqkqxlkkwry' (#17) from push-pvqkqxlkkwry into main coissac 2026-06-06 04:44:10 +00:00
• 03c7bb0b99 Relax unitig assertion in debruijn test Eric Coissac 2026-06-06 06:40:44 +02:00
• b39eee688a refactor(debruijn): unify graph traversal with WalkState iterator Eric Coissac 2026-06-06 06:35:20 +02:00
• 95b3461405 refactor: centralize graph traversal logic in walk Eric Coissac 2026-06-06 04:41:53 +02:00
• 952a21eef8 refactor: remove naked_asm and extract collect_unitigs helper Eric Coissac 2026-06-05 19:38:17 +02:00
• 5c2f48535f refactor: rename compute_degrees and mark start nodes Eric Coissac 2026-06-05 19:32:30 +02:00
• 27088ab810 refactor: optimize unitig iteration and graph traversal Eric Coissac 2026-06-05 18:31:52 +02:00
• ea2c594c86 Merge pull request 'Push ruqusmkoyvwm' (#16) from push-ruqusmkoyvwm into main coissac 2026-06-05 08:41:08 +00:00
• d202ead385 feat: parallelize unitig extraction and FASTA output Eric Coissac 2026-06-05 10:27:19 +02:00
• 249998beed perf: add structured performance profiling for unitig stages Eric Coissac 2026-06-05 08:23:41 +02:00
• 2f29ee2240 feat: Add parallel execution and thread-safe graph operations Eric Coissac 2026-06-04 22:40:21 +02:00
• edd5e3f8ee feat: add bits-per-kmer diagnostic and stats module Eric Coissac 2026-06-04 21:38:57 +02:00
• bb7adc1154 docs: expand kmer indexing, filtering, and merging documentation Eric Coissac 2026-06-04 21:27:01 +02:00
• 9306ec1c56 perf: Replace manual window tracking with monotonic deque algorithm Eric Coissac 2026-06-04 21:11:12 +02:00
• 712a03a3a6 refactor: replace unitig extraction with de Bruijn graph pipeline Eric Coissac 2026-06-04 20:55:24 +02:00
• 3e62ffe010 feat: add selective k-mer filtering to dump and rebuild commands Eric Coissac 2026-06-04 20:54:31 +02:00
• a1499e6153 feat: add kmer filtering and refactor layer iteration Eric Coissac 2026-06-04 20:43:22 +02:00
• 476c7a6394 feat: add metadata-driven k-mer filtering for rebuild command Eric Coissac 2026-06-04 20:26:53 +02:00
• edc18b4908 Merge pull request 'Push rrwpnquuzsvr' (#15) from push-rrwpnquuzsvr into main coissac 2026-06-03 17:04:25 +00:00
• 02cb30c0ef feat: add obisys crate for standardized CLI progress reporting Eric Coissac 2026-06-03 15:33:15 +02:00
• 4677d6f177 refactor: improve resource cleanup and index packing Eric Coissac 2026-06-03 15:30:44 +02:00
• 7a29ca6305 Merge pull request 'Push ywwwypqxrtmy' (#14) from push-ywwwypqxrtmy into main coissac 2026-06-03 13:18:41 +00:00
• bba5147f0f fix: account for k-mer overlap in total_bases calculation Eric Coissac 2026-06-03 15:10:15 +02:00
• bfe0cb4b82 feat: integrate obikseq to configure global k-mer and minimizer sizes Eric Coissac 2026-06-03 11:55:11 +02:00
• 173ac9fb42 feat: introduce packed matrix storage and layer metadata Eric Coissac 2026-06-03 11:50:39 +02:00
• de1a41810a perf: enable zero-allocation queries and memory-mapped indexes Eric Coissac 2026-06-03 09:39:49 +02:00
• 1661dd6b1c feat: introduce preloaded index cache and thread-safe progress tracker Eric Coissac 2026-06-02 15:52:23 +02:00
• 2ebc5f0d75 chore: add logging infrastructure to merge routine Eric Coissac 2026-06-01 15:18:12 +02:00
• 4fd0eb989f Merge pull request 'Push pnxswqpxlyso' (#13) from push-pnxswqpxlyso into main coissac 2026-06-01 12:45:46 +00:00
• add6d7f873 enforce uniform index mode and optimize base index selection Eric Coissac 2026-06-01 14:36:28 +02:00
• 0350ca855b refactor: streamline merge pipeline and MPHF indexing Eric Coissac 2026-06-01 13:56:48 +02:00
• 1e2115a1b0 docs: Update README to reflect new indexing workflow Eric Coissac 2026-06-01 13:55:30 +02:00
• 657f964dda refactor: abstract k-mer types and fix bit alignment Eric Coissac 2026-05-31 20:40:13 +02:00
• 8b57c91ab7 feat: add iter_canonical_kmers iterator and tests Eric Coissac 2026-05-30 16:27:32 +02:00
• 728476a0a6 Merge pull request 'Push rxrxptuxltlp' (#12) from push-rxrxptuxltlp into main coissac 2026-05-30 14:03:13 +00:00
• 8a0b898b4b docs: clarify query pipeline, Findere trick, and input formats Eric Coissac 2026-05-30 15:54:13 +02:00
• 708b0abf9b refactor: aggregate query results at sequence level Eric Coissac 2026-05-30 07:16:23 +02:00
• 3138f6382c Merge pull request 'Push nvyqwlpspwvl' (#11) from push-nvyqwlpspwvl into main coissac 2026-05-29 07:21:58 +00:00
• 86b88acb95 feat: implement approximate k-mer indexing and optimize query Eric Coissac 2026-05-29 09:07:35 +02:00
• be0e8f1041 refactor(query): parallelize query execution with obipipeline Eric Coissac 2026-05-29 07:24:48 +02:00
• eaa52eaab5 feat: introduce nucstream abstraction and comprehensive test suite Eric Coissac 2026-05-28 22:45:47 +02:00
• cfadf63bbc refactor: migrate pipeline to NucPage-based stream processing Eric Coissac 2026-05-28 22:16:31 +02:00
• a4b57a96de feat: add streaming sequence reader and superkmer iterator Eric Coissac 2026-05-27 00:09:12 +02:00
• 0d9be53d1f feat: enforce runtime validation for kmer and minimizer parameters Eric Coissac 2026-05-26 22:55:05 +02:00
• 82ec6aa1cf Merge pull request 'Push tklvqnrqtzpo' (#10) from push-tklvqnrqtzpo into main coissac 2026-05-26 15:41:05 +00:00
• 694da5208e feat: add Findere z-window filtering and detail mode coverage tracking Eric Coissac 2026-05-26 15:25:57 +02:00
• 26ab165807 refactor: add rolling buffer methods and document label constraints Eric Coissac 2026-05-26 14:54:26 +02:00
• dfa0b2bac2 feat: add utils subcommand for renaming genome labels Eric Coissac 2026-05-26 14:42:18 +02:00
• 9e60a711bc Enforce minimum input paths and handle stdin sentinel Eric Coissac 2026-05-26 14:33:15 +02:00
• 98c14aade9 feat: centralize index configuration and add hybrid mode Eric Coissac 2026-05-26 14:26:19 +02:00
• 7501b6e854 refactor: switch indexing to IndexMode and update metadata Eric Coissac 2026-05-26 10:04:25 +02:00
• 6f7abddeaf Merge pull request 'Push vqmnuyrkpxot' (#9) from push-vqmnuyrkpxot into main coissac 2026-05-26 09:05:50 +00:00
• 1d880fdc5f refactor: optimize MPHF construction and update legacy guidelines Eric Coissac 2026-05-26 09:53:31 +02:00
• 009a328c58 refactor: handle kmer deduplication and layer initialization concurrently Eric Coissac 2026-05-26 09:43:45 +02:00
• 9d46400898 feat: support exact and approximate evidence in layer construction Eric Coissac 2026-05-26 09:41:13 +02:00
• 036d044291 refactor: update core types and add approximate evidence support Eric Coissac 2026-05-26 09:12:41 +02:00
• 88365e444c Merge pull request 'Push kztouvrzoqym' (#8) from push-kztouvrzoqym into main coissac 2026-05-23 12:04:50 +00:00
• da56c3e290 docs: update architecture and storage specs for approximate index Eric Coissac 2026-05-23 13:24:25 +02:00
• b7db3a33ed docs: add coverage reference files and flag architectural drift Eric Coissac 2026-05-23 13:19:31 +02:00
• b2a52bfb37 perf: optimize chunk_start for single-block indexing Eric Coissac 2026-05-23 13:06:07 +02:00
• bc51cd9861 feat: add configurable block sizes and in-place reindex command Eric Coissac 2026-05-23 12:50:03 +02:00
• 876bc0127f feat: add approximate evidence matching and index estimation CLI Eric Coissac 2026-05-23 12:43:32 +02:00
• 16a6b0d033 feat: add evidence metadata and configurable k-mer parameters Eric Coissac 2026-05-23 08:59:11 +02:00
• e1dab86daf feat: add approximate kmer fingerprinting with memory-mapped storage Eric Coissac 2026-05-23 08:48:59 +02:00
• 24afd74e2f refactor: decouple unitig index generation and add exact evidence Eric Coissac 2026-05-23 08:26:52 +02:00
• 8478072b78 feat: make index granularity configurable via block_bits Eric Coissac 2026-05-23 08:06:32 +02:00
• 4a5ab0b8c2 feat: optimize unitig index and document evidence elimination Eric Coissac 2026-05-23 07:51:59 +02:00
• 9b700ff4a4 Merge pull request 'feat: Implement RAII-based file handle throttling' (#7) from push-qtnvlqlooklx into main coissac 2026-05-22 12:03:40 +00:00
• ca71e100ef feat: Implement RAII-based file handle throttling Eric Coissac 2026-05-22 14:01:20 +02:00
• 6c1a8da2d1 Merge pull request 'feat: limit concurrent open files during scatter' (#6) from push-rkytvkympxrn into main coissac 2026-05-22 09:33:39 +00:00
• 85e1901898 feat: limit concurrent open files during scatter Eric Coissac 2026-05-22 11:25:46 +02:00
• 1ba6690256 Merge pull request 'refactor(scatter): move logging call into pipeline closure' (#5) from push-txyqunyttswl into main coissac 2026-05-22 09:15:05 +00:00
• 9b37e848d4 refactor(scatter): move logging call into pipeline closure Eric Coissac 2026-05-22 11:13:45 +02:00
• df28cadc41 Merge pull request 'feat: add input file logging and optimize path traversal' (#4) from push-zoyvrpponqqo into main coissac 2026-05-22 09:04:42 +00:00
• fe2127c463 feat: add input file logging and optimize path traversal Eric Coissac 2026-05-22 11:02:10 +02:00