95 Commits

Author	SHA1	Message	Date
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	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	86b7dd424a	avoid misassemblies; better polyploidy graph	2023-03-22 12:23:53 -04:00
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	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	46391eba26	fix bubble popping bugs	2023-01-15 22:29:20 -05:00
chhylp123	0613b18af9	r493 ->HiC/UL/Trans	2023-01-11 20:38:45 -05:00
chhylp123	fc76af1285	fixed gap filling with UL	2022-11-25 11:46:37 -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	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	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	89e0d1aafa	UL graph with graph cleaning	2022-08-02 15:48:16 -04:00
chhylp123	33afa25398	UL graph done	2022-07-24 18:13:16 -04:00
chhylp123	e8399b18f1	fixed duplicated chaining issue	2022-05-03 17:35:43 -04:00
chhylp123	fdf24d5589	fix memory bug/logic bug	2022-05-01 00:37:32 -04:00
chhylp123	3064e1373b	better uovlp saving	2022-04-22 23:10:21 -04:00
chhylp123	9c79bdfe7f	UL_gdp	2022-04-13 16:15:03 -04:00
chhylp123	60236cd967	debug uc_block_t	2022-03-21 22:00:30 -04:00
chhylp123	d3b9de4120	new gchain	2022-03-16 01:13:27 -04:00
chhylp123	9c6a3607d1	intergration correctio	2022-03-01 20:25:53 -05:00
chhylp123	0ce5a7ba5b	integration/print het sites	2022-01-17 18:29:48 -05:00
chhylp123	9ec286e64e	new ul	2021-12-11 14:55:36 -05:00
chhylp123	1e2a9518e5	print dup log	2021-11-29 15:11:02 -05:00
chhylp123	763634e1a9	kpt_dup	2021-11-28 19:35:32 -05:00
chhylp123	7dd4a848b9	debug graph	2021-09-26 13:51:13 -04:00
chhylp123	ab80851b94	mempcpy -> memcpy	2021-09-12 17:43:43 -04:00
chhylp123	809ca18dda	r373	2021-09-10 17:17:44 -04:00
chhylp123	37b07e4d33	better seeding	2021-08-22 09:53:34 -04:00
chhylp123	5a400af39d	r342-misjoin	2021-06-19 14:09:09 -04:00
chhylp123	aa164949f2	backup phasing	2021-05-31 04:19:05 -04:00
chhylp123	e774a83be2	debug mbg	2021-05-30 09:02:25 -04:00
chhylp123	a39f01f4d8	haplotype popping	2021-05-24 19:43:50 -04:00
chhylp123	9e6dde7fb2	backpup	2021-05-22 10:48:49 -04:00
chhylp123	b12e008416	new somatic variant popping	2021-05-19 09:52:40 -04:00
chhylp123	be8e1e3117	sc debug	2021-05-17 00:12:41 -04:00
chhylp123	4105dd360e	correction	2021-05-11 13:01:06 -04:00
chhylp123	7918396d21	collect contig alignment + renew_utg bug fixed	2021-05-09 17:47:50 -04:00
chhylp123	9ea4f6917f	resolve centromere	2021-05-06 07:59:51 -04:00
chhylp123	7b07e355b7	bug fix for bubble scanning	2021-04-23 20:40:43 -04:00
chhylp123	475ebb8075	keep long range information	2021-04-20 01:29:15 -04:00
chhylp123	f8ee584291	code clean	2021-04-16 20:28:48 -04:00
chhylp123	1e86e3dc02	best flipping	2021-04-14 18:50:20 -04:00