48 Commits

Author	SHA1	Message	Date
chhylp123	25d6857d44	r499->false duplications	2023-01-17 04:49:56 -05:00
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
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	dbc72b8c2d	has bug multiple threads	2021-12-28 21:48:41 -05:00
chhylp123	8a0ec3d575	change ug extraction	2021-12-12 20:59:48 -05:00
chhylp123	908b4f3786	bug fix	2021-10-10 14:47:16 -04:00
chhylp123	cb320b88f3	debug ul	2021-10-10 13:37:32 -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	e230b3a55f	0.16.0 release	2021-08-22 21:58:00 -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	8e98fb2276	Merge branch 'master' into dev-lh3	2021-03-02 19:27:44 -05:00
chhylp123	fda13cb0e4	update -z	2021-02-02 12:45:50 -05:00
Heng Li	61befd357a	r333: also subsample high-freq mz during indexing	2021-01-22 23:17:25 -05:00
Heng Li	da672118e5	r330: unimap heuristic for mz sampling	2021-01-21 11:05:37 -05:00
chhylp123	3a1a3750e9	Merge branch 'master' of https://github.com/chhylp123/Long_read_assembly	2020-11-16 01:49:07 -05:00
chhylp123	ab073aa1fc	hic first	2020-11-14 23:35:32 -05:00
Heng Li	f02eb66e6a	r326: select high-occ k-mers (experimental)	2020-10-29 22:36:54 -04:00
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
Heng Li	eddb8173da	added --min-hist-cnt for #49	2020-10-26 16:28:30 -04:00
chhylp123	89fcb35a64	for debugging	2020-10-11 14:32:33 -04:00
chhylp123	03cf0d475c	save bfore multiple overlaps	2020-08-23 08:46:33 -04:00
chhylp123	a25c37ed89	update k-mer peaks	2020-07-07 13:20:25 -04:00
Heng Li	c41aae0630	r211: added --write-paf/--write-ec/--skip-triobin	2020-04-08 22:32:54 -04:00
Heng Li	8efcdefcaf	r207: multiple input files were not working	2020-04-07 12:40:10 -04:00
Heng Li	adbc65feda	r201: automatically adjust -N	2020-04-05 22:43:01 -04:00
Heng Li	f0c53e9948	r192: estimate buffer memory	2020-04-05 11:17:12 -04:00
Heng Li	4fa3cbfd46	double the chunk size	2020-03-27 22:46:51 -04:00
Heng Li	5e16483b43	option to skip k-mer filtering	2020-03-27 22:32:39 -04:00
Heng Li	cb20e50219	disabled progress report	2020-03-27 17:05:56 -04:00
Heng Li	1bb174a04e	fixed missing read names ... Overlapping not working yet (now confirmed)	2020-03-27 12:51:08 -04:00
Heng Li	7271c106e4	reverted to the older k_mer_hit definition	2020-03-27 10:40:31 -04:00
Heng Li	10ed8b36ec	implemented ha_pt_get()	2020-03-26 23:00:00 -04:00
Heng Li	4aa4ebaf96	more unused code	2020-03-26 17:57:39 -04:00
Heng Li	387d6336d8	read from read store	2020-03-26 15:17:49 -04:00
Heng Li	0dd927bdce	write to hifiasm read store	2020-03-26 14:23:17 -04:00
Heng Li	c3bbaa8a39	prepare for integration with hifiasm	2020-03-26 11:33:52 -04:00
Heng Li	60d94790a2	fixed a memory leak	2020-03-25 23:52:09 -04:00
Heng Li	ff8194d291	position indexing apparently working	2020-03-25 23:44:15 -04:00
Heng Li	716713685c	renamed files for code cleanup	2020-03-25 19:59:17 -04:00