52 Commits

Author	SHA1	Message	Date
chhylp123	4889f1c6d8	fix high-coverage issue for ONT	2024-12-07 20:02:57 -05:00
chhylp123	184eb0a9fe	fix the memory issue	2024-12-06 05:17:30 -05:00
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	d5f8a8a6c0	new ec model	2024-06-30 19:53:51 -04:00
chhylp123	86b7dd424a	avoid misassemblies; better polyploidy graph	2023-03-22 12:23:53 -04:00
chhylp123	f2da12a2ad	508 —> futhur graph cleaning	2023-02-12 22:49:12 -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	1d0562ebd1	done second alignment	2022-10-09 16:59:54 -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	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	fdf24d5589	fix memory bug/logic bug	2022-05-01 00:37:32 -04:00
chhylp123	0ce5a7ba5b	integration/print het sites	2022-01-17 18:29:48 -05:00
chhylp123	7af0d85258	backup	2021-12-29 21:22:43 -05:00
chhylp123	ed814abf35	before branch	2021-09-16 17:16:30 -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	17b5cb21d3	tmp macro	2021-08-30 09:30:48 -04:00
chhylp123	37b07e4d33	better seeding	2021-08-22 09:53:34 -04:00
chhylp123	bfff640a82	dp opt	2021-08-12 11:16:10 -04:00
chhylp123	6ea66e1290	resolve conflicts	2021-07-27 20:11:22 -04:00
chhylp123	3c8a933b8a	Merge remote-tracking branch 'origin/dev-lh3'	2021-07-27 19:50:29 -04:00
chhylp123	e774a83be2	debug mbg	2021-05-30 09:02:25 -04:00
Heng Li	3b8f73fbab	r332: increased mz sample dist from 200 to 500	2021-01-22 10:31:29 -05:00
Heng Li	da672118e5	r330: unimap heuristic for mz sampling	2021-01-21 11:05:37 -05:00
Heng Li	f37c4e29fa	a bit refactoring for the next change	2020-10-29 18:24:47 -04:00
Heng Li	ef8c047559	removed unused ha_sketch	2020-10-29 11:28:43 -04:00
chhylp123	89fcb35a64	for debugging	2020-10-11 14:32:33 -04:00
chhylp123	724990cbe7	freeze-r304	2020-08-23 23:34:36 -04:00
chhylp123	03cf0d475c	save bfore multiple overlaps	2020-08-23 08:46:33 -04:00
chhylp123	ace34ae2b8	for high-het and coverage	2020-07-28 13:07:35 -04:00
Heng Li	f6ea45b58a	r251: always keep the best hits	2020-05-08 00:40:53 -04:00
Heng Li	e544360043	r250: fixed a bug in selecting top chains	2020-05-07 14:49:49 -04:00
Heng Li	331e437c72	r248: contained reads not handled properly	2020-05-03 00:27:53 -04:00
Heng Li	22b681b830	r228: resolved a compiler warning	2020-04-12 09:56:50 -04:00
Heng Li	4d7600361c	r226b: prefer unique anchors	2020-04-11 22:28:21 -04:00
Heng Li	c41aae0630	r211: added --write-paf/--write-ec/--skip-triobin	2020-04-08 22:32:54 -04:00
Heng Li	f0c53e9948	r192: estimate buffer memory	2020-04-05 11:17:12 -04:00
Heng Li	968b4caef9	r181: limit the max number of chains	2020-04-02 21:55:00 -04:00
Heng Li	3838482851	moved sorting to anchor.cpp for future changes	2020-04-02 19:18:29 -04:00
Heng Li	b7e5d1c4d3	r176: enabled the minimap2 chaining heuristic	2020-04-01 22:06:14 -04:00
Heng Li	7079a9f306	working on mid-sized test example	2020-03-27 16:55:28 -04:00
Heng Li	bd89bd500c	add disabled debugging code	2020-03-27 14:03:36 -04:00
Heng Li	30a70bc307	fixed wrong coordinate	2020-03-27 13:45:09 -04:00
Heng Li	1bb174a04e	fixed missing read names ... Overlapping not working yet (now confirmed)	2020-03-27 12:51:08 -04:00