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• 06cf12a32a r942 for temp release hybrid_v1 chhylp123 2026-05-30 23:20:10 -04:00
• bca2394b69 unsucessful hpc mark chhylp123 2026-05-15 19:02:16 -04:00
• 7884b5ad88 regen_scb chhylp123 2026-05-03 03:34:23 -04:00
• f5078f7b23 seperate phase dp to ont/hifi chhylp123 2026-04-15 11:59:09 -04:00
• 6b026f0caa fast dp hybrid chhylp123 2026-04-14 14:31:02 -04:00
• ba8627fb23 phasing speedup chhylp123 2026-04-11 22:33:18 -04:00
• 815d709fb9 fall back to avx2 chhylp123 2026-04-01 22:28:54 -04:00
• a137a6b06f r878 chhylp123 2026-03-28 11:02:52 -04:00
• e53fc786bd fix slow running time vs r726 chhylp123 2026-03-27 15:37:44 -04:00
• aa4d12b1c6 simd version 0 chhylp123 2026-03-24 17:54:36 -04:00
• 9a2884f518 backup avx chhylp123 2026-03-20 16:06:06 -04:00
• 5e5a1568ed error est funcion chhylp123 2026-03-17 17:27:48 -04:00
• c0478830e6 err_estimate chhylp123 2026-03-01 08:51:53 -05:00
• 2fa4ef224f updating final overlapping chhylp123 2026-02-17 18:07:49 -05:00
• 86311effb9 running time bug fixed chhylp123 2026-02-16 10:46:28 -05:00
• 53e1b150c3 bug fixed for memory leak chhylp123 2026-02-12 16:47:32 -05:00
• 67877deed3 r852 -> hybrid correction chhylp123 2026-02-11 16:38:57 -05:00
• d6ba102d42 r852 -> hybrid correction chhylp123 2026-02-11 16:38:27 -05:00
• ec9a8b222d add new options for ont assembly master 0.25.0 chhylp123 2025-03-18 12:29:48 -04:00
• b3b18ab1d0 r721 chhylp123 2025-03-14 01:40:21 -04:00
• a96191560e eliminate SVs chhylp123 2025-03-10 16:09:02 -04:00
• 79387d081f update readme chhylp123 2025-01-31 20:34:12 -05:00
• 4733ef5011 update readme for ont chhylp123 2025-01-31 20:27:22 -05:00
• 2c77b3c87e ont overlapping chhylp123 2024-12-21 03:17:17 -05:00
• 3067771783 update for low coverge data 0.24.0 chhylp123 2024-12-16 06:25:31 -05:00
• 4889f1c6d8 fix high-coverage issue for ONT 0.23.0 chhylp123 2024-12-07 20:02:57 -05:00
• dbdef7ff63 fix Print_H 0.22.0 chhylp123 2024-12-06 05:29:19 -05:00
• 184eb0a9fe fix the memory issue chhylp123 2024-12-06 05:17:30 -05:00
• 676385cf8e ont simplex support 0.21.0 chhylp123 2024-11-27 13:27:13 -05:00
• 80fa5ed436 ONT EC chhylp123 2024-11-12 23:53:29 -05:00
• 6de4e14782 update before fly HPC chhylp123 2024-10-29 14:59:52 -04:00
• ade800990e update for reference read hpc chhylp123 2024-10-27 13:22:06 -04:00
• fc98214321 update cite 0.20.0 chhylp123 2024-10-14 12:35:48 -04:00
• 382adb89c5 update README chhylp123 2024-10-14 12:30:48 -04:00
• 6e33d972d0 update README chhylp123 2024-10-14 12:29:35 -04:00
• 39a30a8d55 update README chhylp123 2024-10-14 12:23:57 -04:00
• b01614fd71 update README chhylp123 2024-10-13 19:07:51 -04:00
• 63d51c3441 update README chhylp123 2024-10-13 19:06:01 -04:00
• 49dd83df2a fix memory issue chhylp123 2024-10-13 18:47:05 -04:00
• e8b18560a5 0.20.0-r631 chhylp123 2024-10-09 17:09:10 -04:00
• d5f8a8a6c0 new ec model chhylp123 2024-06-30 19:53:51 -04:00
• 70fd9a0b1f keeping more telomeres 0.19.9 chhylp123 2024-05-06 04:02:20 -04:00
• 73dd5eeb5b gen_telo_end_t chhylp123 2024-04-28 15:11:21 -04:00
• 358b090e20 fix scaf bugs chhylp123 2024-04-27 07:58:49 -04:00
• b992a07d05 inbananced coverage hifiasm_dev_debug chhylp123 2024-04-02 10:40:11 -04:00
• 1ac574adc7 Merge pull request #553 from chhylp123/hifiasm_dev_debug 0.19.8 chhylp123 2023-11-06 00:10:06 -05:00
• 61ceb3a4e1 fix bubble issue chhylp123 2023-11-06 00:09:38 -05:00
• 7f6d36b2c4 Merge pull request #540 from chhylp123/hifiasm_dev_debug chhylp123 2023-10-22 13:24:28 -04:00
• 4ca8951f9d fix bug for gen_contain_consensus_chain chhylp123 2023-10-22 13:23:27 -04:00
• 40e2a48706 Merge pull request #535 from chhylp123/hifiasm_dev_debug 0.19.7 chhylp123 2023-10-10 12:41:10 -04:00
• 281ae6ba89 add scaffolding chhylp123 2023-10-10 12:40:29 -04:00
• e974b22ac0 Merge pull request #521 from chhylp123/hifiasm_dev_debug chhylp123 2023-09-15 13:00:13 -04:00
• c7685e6f19 checkpoint for scaffolding chhylp123 2023-09-15 12:58:34 -04:00
• 94a284b430 Merge pull request #503 from chhylp123/hifiasm_dev_debug 0.19.6 chhylp123 2023-08-17 19:59:13 -04:00
• 858b95a3bb disable multiple assertions chhylp123 2023-08-17 19:58:35 -04:00
• 30d2ee065e Merge pull request #482 from chhylp123/hifiasm_dev_debug chhylp123 2023-07-19 19:12:10 -04:00
• 64091a76a5 fix filter_short_ulalignments chhylp123 2023-07-19 19:11:37 -04:00
• d91fc50058 Merge pull request #462 from chhylp123/hifiasm_dev_debug chhylp123 2023-05-31 14:55:16 -04:00
• adeb2c603d trio-dual/bug for hic phasing chhylp123 2023-05-31 14:54:50 -04:00
• abff5fae04 Merge pull request #457 from chhylp123/hifiasm_dev_debug chhylp123 2023-05-12 20:57:45 -04:00
• 44475e2665 remove ksw2 from makefile chhylp123 2023-05-12 20:57:11 -04:00
• 2cc990ed22 Merge pull request #455 from chhylp123/hifiasm_dev_debug chhylp123 2023-05-12 11:32:03 -04:00
• 2c18ec30da fix memory leak of print_utg chhylp123 2023-05-12 11:31:34 -04:00
• 5bddae4ae9 Merge pull request #446 from chhylp123/hifiasm_dev_debug 0.19.5 chhylp123 2023-04-17 19:58:31 -04:00
• 18b649aadb fixed missing/false duplication for diploid asm chhylp123 2023-04-17 19:58:00 -04:00
• fbfcf72eb3 Merge pull request #445 from chhylp123/hifiasm_dev_debug chhylp123 2023-04-14 16:44:10 -04:00
• 0efcc14499 fix chain spliting bug chhylp123 2023-04-14 16:43:41 -04:00
• 84e642d20d fix bubble on-the-fly chhylp123 2023-04-13 10:16:14 -04:00
• b49b4a6cc7 Merge pull request #438 from chhylp123/hifiasm_dev_debug 0.19.4 chhylp123 2023-04-06 23:18:26 -04:00
• 7e855ba5e2 update README chhylp123 2023-04-06 23:16:59 -04:00
• 5df5892f33 update for rescuing missing contigs chhylp123 2023-04-06 23:14:41 -04:00
• 00959dfdd9 Merge pull request #430 from chhylp123/hifiasm_dev_debug 0.19.3 chhylp123 2023-03-22 12:26:41 -04:00
• 503cd0f7cc 0.19.2->0.19.3 chhylp123 2023-03-22 12:25:39 -04:00
• 00ad7458c3 Merge pull request #429 from chhylp123/hifiasm_dev_debug chhylp123 2023-03-22 12:24:31 -04:00
• 86b7dd424a avoid misassemblies; better polyploidy graph chhylp123 2023-03-22 12:23:53 -04:00
• b763e1ff76 Merge pull request #422 from chhylp123/hifiasm_dev_debug 0.19.2 chhylp123 2023-03-13 15:44:45 -04:00
• d4773a497f disable postjoin for the ul assembly chhylp123 2023-03-13 15:43:22 -04:00
• 7bb366688e Merge pull request #421 from chhylp123/hifiasm_dev_debug 0.19.1 chhylp123 2023-03-13 11:14:38 -04:00
• f67faa9c34 path-max and path-min to avoid misassemblies chhylp123 2023-03-13 11:13:57 -04:00
• 3407c7029e coverage adjustment for polyploidy chhylp123 2023-03-12 17:02:29 -04:00
• f69166ee3b Merge pull request #420 from chhylp123/hifiasm_dev_debug chhylp123 2023-03-10 23:44:34 -05:00
• 2218bac8aa clean output chhylp123 2023-03-10 23:42:29 -05:00
• b533067835 enable dbg-ovec chhylp123 2023-03-10 23:30:24 -05:00
• fa663a9680 Merge pull request #419 from chhylp123/hifiasm_dev_debug 0.19.0 chhylp123 2023-03-10 19:34:50 -05:00
• 384b721d84 clean output chhylp123 2023-03-10 15:46:23 -05:00
• 8b79a3f22e disable function for tangles with low-coverage ul chhylp123 2023-03-10 15:34:10 -05:00
• af4be8ca1a disable integer correction; disable contain dedup chhylp123 2023-03-10 09:12:07 -05:00
• 85c643e85d clean contained read; fixed for deep_graph_clean chhylp123 2023-03-07 15:28:24 -05:00
• 8a00c6c5f4 Merge pull request #414 from chhylp123/hifiasm_dev_debug chhylp123 2023-02-27 09:36:46 -05:00
• a0f2f70d91 better resolution for complex regions chhylp123 2023-02-27 09:35:50 -05:00
• ad4ff5550b Merge pull request #411 from chhylp123/hifiasm_dev_debug 0.18.9 chhylp123 2023-02-24 00:37:36 -05:00
• 04f660fd8c bug fixed for mask calculation chhylp123 2023-02-24 00:36:52 -05:00
• dd5f368fe6 Merge pull request #409 from chhylp123/hifiasm_dev_debug 0.18.8 chhylp123 2023-02-21 20:23:31 -05:00
• 2b4b4f29e0 r525 chhylp123 2023-02-21 20:22:56 -05:00
• 8ea2d5a622 r523-phasing-across chains chhylp123 2023-02-21 15:44:45 -05:00
• 27f77dca29 Merge pull request #401 from chhylp123/hifiasm_dev_debug chhylp123 2023-02-20 23:42:20 -05:00
• 7d5c793109 additional cluster for phasing chhylp123 2023-02-20 23:38:27 -05:00
• 3abd3793fb clean graph alignment chhylp123 2023-02-20 14:50:55 -05:00
• b55e4396d2 prt_dbg_gfa -> before transitive reduction chhylp123 2023-02-17 11:00:15 -05:00
• fc598d71f6 0.18.6 -> 0.18.7 chhylp123 2023-02-16 12:16:24 -05:00