53 Commits

Author	SHA1	Message	Date
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	86b7dd424a	avoid misassemblies; better polyploidy graph	2023-03-22 12:23:53 -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	2218bac8aa	clean output	2023-03-10 23:42:29 -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	2b4b4f29e0	r525	2023-02-21 20:22:56 -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	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	0613b18af9	r493 ->HiC/UL/Trans	2023-01-11 20:38:45 -05:00
chhylp123	a674110b23	fixed het/hom node bugs	2022-12-08 03:07:14 -05:00
chhylp123	a3b72457f0	cleaner assembly graph	2022-12-06 09:52:00 -05:00
chhylp123	786f8bdff0	r465	2022-12-02 09:40:25 -05:00
chhylp123	a4d6cebc32	slightly better assembly graph	2022-11-28 14:42:48 -05:00
chhylp123	fc76af1285	fixed gap filling with UL	2022-11-25 11:46:37 -05:00
chhylp123	553a8745cc	bugs for bubble/hom assembly	2022-11-17 18:01:08 -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	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	2443e63ef5	done chaining	2022-10-08 14:51:03 -04:00
chhylp123	8b7ca5f0c3	revised HiFi phasing	2022-08-23 10:36:35 -04:00
chhylp123	54465dd9ac	tangle resolved	2022-08-16 23:35:56 -04:00
chhylp123	89e0d1aafa	UL graph with graph cleaning	2022-08-02 15:48:16 -04:00
chhylp123	91de382bde	before contain keeping	2022-07-27 10:41:57 -04:00
chhylp123	239f087af0	exact ul ovlp	2022-07-26 20:57:34 -04:00
chhylp123	33afa25398	UL graph done	2022-07-24 18:13:16 -04:00
chhylp123	138610b049	ul coordinates fixed	2022-06-25 21:52:56 -04:00
chhylp123	a82e05c9f2	fix gap alignment extention	2022-06-23 22:11:28 -04:00
chhylp123	3934167770	integer correction update	2022-06-20 01:51:19 -04:00
chhylp123	a21bc8a336	correction done	2022-06-18 22:42:01 -04:00
chhylp123	7cf6d82115	init poa	2022-06-15 16:58:23 -04:00
chhylp123	98bb89227e	integer correction	2022-06-07 16:56:28 -04:00
chhylp123	8a2bb0b112	memory debugging	2022-05-04 20:22:50 -04:00
chhylp123	e8399b18f1	fixed duplicated chaining issue	2022-05-03 17:35:43 -04:00
chhylp123	8138941a26	new realignment	2022-05-03 00:59:24 -04:00
chhylp123	fdf24d5589	fix memory bug/logic bug	2022-05-01 00:37:32 -04:00