260 Commits

Author	SHA1	Message	Date
chhylp123	ec9a8b222d	add new options for ont assembly	2025-03-18 12:29:48 -04:00
chhylp123	b3b18ab1d0	r721	2025-03-14 01:40:21 -04:00
chhylp123	a96191560e	eliminate SVs	2025-03-10 16:09:02 -04:00
chhylp123	4733ef5011	update readme for ont	2025-01-31 20:27:22 -05:00
chhylp123	2c77b3c87e	ont overlapping	2024-12-21 03:17:17 -05:00
chhylp123	3067771783	update for low coverge data	2024-12-16 06:25:31 -05:00
chhylp123	4889f1c6d8	fix high-coverage issue for ONT	2024-12-07 20:02:57 -05:00
chhylp123	dbdef7ff63	fix Print_H	2024-12-06 05:29:19 -05:00
chhylp123	184eb0a9fe	fix the memory issue	2024-12-06 05:17:30 -05:00
chhylp123	676385cf8e	ont simplex support	2024-11-27 13:27:13 -05:00
chhylp123	80fa5ed436	ONT EC	2024-11-12 23:53:29 -05:00
chhylp123	6de4e14782	update before fly HPC	2024-10-29 14:59:52 -04:00
chhylp123	ade800990e	update for reference read hpc	2024-10-27 13:22:06 -04:00
chhylp123	49dd83df2a	fix memory issue	2024-10-13 18:47:05 -04:00
chhylp123	e8b18560a5	0.20.0-r631	2024-10-09 17:09:10 -04:00
chhylp123	70fd9a0b1f	keeping more telomeres	2024-05-06 04:02:20 -04:00
chhylp123	73dd5eeb5b	gen_telo_end_t	2024-04-28 15:11:21 -04:00
chhylp123	358b090e20	fix scaf bugs	2024-04-27 07:58:49 -04:00
chhylp123	61ceb3a4e1	fix bubble issue	2023-11-06 00:09:38 -05:00
chhylp123	4ca8951f9d	fix bug for gen_contain_consensus_chain	2023-10-22 13:23:27 -04:00
chhylp123	281ae6ba89	add scaffolding	2023-10-10 12:40:29 -04:00
chhylp123	c7685e6f19	checkpoint for scaffolding	2023-09-15 12:58:34 -04:00
chhylp123	858b95a3bb	disable multiple assertions	2023-08-17 19:58:35 -04:00
chhylp123	64091a76a5	fix filter_short_ulalignments	2023-07-19 19:11:37 -04:00
chhylp123	adeb2c603d	trio-dual/bug for hic phasing	2023-05-31 14:54:50 -04:00
chhylp123	44475e2665	remove ksw2 from makefile	2023-05-12 20:57:11 -04:00
chhylp123	2c18ec30da	fix memory leak of print_utg	2023-05-12 11:31:34 -04:00
chhylp123	18b649aadb	fixed missing/false duplication for diploid asm	2023-04-17 19:58:00 -04:00
chhylp123	0efcc14499	fix chain spliting bug	2023-04-14 16:43:41 -04:00
chhylp123	84e642d20d	fix bubble on-the-fly	2023-04-13 10:16:14 -04:00
chhylp123	5df5892f33	update for rescuing missing contigs	2023-04-06 23:14:41 -04:00
chhylp123	503cd0f7cc	0.19.2->0.19.3	2023-03-22 12:25:39 -04:00
chhylp123	86b7dd424a	avoid misassemblies; better polyploidy graph	2023-03-22 12:23:53 -04:00
chhylp123	d4773a497f	disable postjoin for the ul assembly	2023-03-13 15:43:22 -04:00
chhylp123	f67faa9c34	path-max and path-min to avoid misassemblies	2023-03-13 11:13:57 -04:00
chhylp123	3407c7029e	coverage adjustment for polyploidy	2023-03-12 17:02:29 -04:00
chhylp123	b533067835	enable dbg-ovec	2023-03-10 23:30:24 -05:00
chhylp123	384b721d84	clean output	2023-03-10 15:46:23 -05:00
chhylp123	8b79a3f22e	disable function for tangles with low-coverage ul	2023-03-10 15:34:10 -05:00
chhylp123	af4be8ca1a	disable integer correction; disable contain dedup	2023-03-10 09:12:07 -05:00
chhylp123	85c643e85d	clean contained read; fixed for deep_graph_clean	2023-03-07 15:28:24 -05:00
chhylp123	a0f2f70d91	better resolution for complex regions	2023-02-27 09:35:50 -05:00
chhylp123	04f660fd8c	bug fixed for mask calculation	2023-02-24 00:36:52 -05:00
chhylp123	2b4b4f29e0	r525	2023-02-21 20:22:56 -05:00
chhylp123	8ea2d5a622	r523-phasing-across chains	2023-02-21 15:44:45 -05:00
chhylp123	7d5c793109	additional cluster for phasing	2023-02-20 23:38:27 -05:00
chhylp123	3abd3793fb	clean graph alignment	2023-02-20 14:50:55 -05:00
chhylp123	b55e4396d2	prt_dbg_gfa -> before transitive reduction	2023-02-17 11:00:15 -05:00
chhylp123	fc598d71f6	0.18.6 -> 0.18.7	2023-02-16 12:16:24 -05:00
chhylp123	286b897881	r513	2023-02-16 00:04:06 -05:00