84 Commits

Author	SHA1	Message	Date
chhylp123	358b090e20	fix scaf bugs	2024-04-27 07:58:49 -04:00
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	5df5892f33	update for rescuing missing contigs	2023-04-06 23:14:41 -04:00
chhylp123	86b7dd424a	avoid misassemblies; better polyploidy graph	2023-03-22 12:23:53 -04:00
chhylp123	3407c7029e	coverage adjustment for polyploidy	2023-03-12 17:02:29 -04:00
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	04f660fd8c	bug fixed for mask calculation	2023-02-24 00:36:52 -05:00
chhylp123	3abd3793fb	clean graph alignment	2023-02-20 14:50:55 -05:00
chhylp123	286b897881	r513	2023-02-16 00:04:06 -05:00
chhylp123	f2da12a2ad	508 —> futhur graph cleaning	2023-02-12 22:49:12 -05:00
chhylp123	1166b92eb4	r502->additional alignment	2023-01-25 09:39:41 -05:00
chhylp123	db2edc0ffb	fix exit(1) for bin_only	2023-01-23 15:25:01 -05:00
chhylp123	25d6857d44	r499->false duplications	2023-01-17 04:49:56 -05:00
chhylp123	0613b18af9	r493 ->HiC/UL/Trans	2023-01-11 20:38:45 -05:00
chhylp123	a3b72457f0	cleaner assembly graph	2022-12-06 09:52:00 -05:00
chhylp123	9a454576e1	fixed memory issue within gen_single_khit	2022-11-25 20:49:14 -05:00
chhylp123	152bae2dfb	fix utg el bug	2022-11-17 12:18:40 -05:00
chhylp123	9831afaf26	code clean	2022-11-17 09:31:56 -05:00
chhylp123	2c7b164f11	tmp cache	2022-11-10 19:37:52 -05:00
chhylp123	46acc8a2f6	version with wrong realignment	2022-11-07 02:35:26 -05:00
chhylp123	612c1ab712	cuttoff before debugging	2022-11-05 09:03:23 -04:00
chhylp123	e66c003b65	cleaner graph	2022-11-01 21:44:13 -04:00
chhylp123	f4b6223fde	cutoff-r426-avoid-tip	2022-10-31 15:18:52 -04:00
chhylp123	3d1787e57a	ul_refine_alignment	2022-10-29 17:15:19 -04:00
chhylp123	249bee7304	done contain clean	2022-10-27 17:05:46 -04:00
chhylp123	df3e0eeaa3	read extract	2022-10-19 13:23:25 -04:00
chhylp123	3d65bef9de	adjusted chain sc	2022-10-09 18:14:07 -04:00
chhylp123	1d0562ebd1	done second alignment	2022-10-09 16:59:54 -04:00
chhylp123	2443e63ef5	done chaining	2022-10-08 14:51:03 -04:00
chhylp123	f92cef38f2	uodate gchain	2022-10-07 15:14:08 -04:00
chhylp123	68a74fb16d	cigar collect	2022-10-02 14:38:49 -04:00
chhylp123	41437764f0	before window filling	2022-10-01 23:42:38 -04:00
chhylp123	bbd3394b4a	lack final alignment	2022-10-01 19:53:02 -04:00
chhylp123	20a7dac82a	backup for minimizer	2022-09-28 11:16:09 -04:00
chhylp123	236bc7b9ee	backup for minimizer	2022-09-28 11:15:29 -04:00
chhylp123	a297105258	cal_exz_infi	2022-09-24 16:16:54 -04:00
chhylp123	38e00d2086	shared seeds	2022-09-23 22:17:38 -04:00
chhylp123	f4cc895fa0	update ed	2022-09-20 22:48:59 -04:00
chhylp123	4e7bb7eeb9	fix cigar	2022-09-18 23:17:58 -04:00
chhylp123	5da05f308f	extend ed alignment	2022-09-13 17:29:27 -04:00
chhylp123	ee51a6dddc	seperate alignment	2022-09-04 00:18:51 -04:00
chhylp123	cc16626dfa	debug cigar_offset	2022-09-01 23:16:08 -04:00
chhylp123	7b89478b2e	code clean	2022-08-28 02:39:05 -04:00
chhylp123	8b7ca5f0c3	revised HiFi phasing	2022-08-23 10:36:35 -04:00
chhylp123	33afa25398	UL graph done	2022-07-24 18:13:16 -04:00