48 Commits

Author	SHA1	Message	Date
chhylp123	03cf0d475c	save bfore multiple overlaps	2020-08-23 08:46:33 -04:00
Heng Li	946a0f4115	r238: got rid of LIS chaining	2020-04-13 14:44:10 -04:00
Heng Li	b333addb6c	r237: fall back to DP chaining more often	2020-04-13 08:39:05 -04:00
Heng Li	2c4de3a326	r230: the first anchor score was not adjusted	2020-04-12 10:39:42 -04:00
Heng Li	75a89c214d	r229: LIS score is still not exactly right	2020-04-12 10:19:28 -04:00
Heng Li	4d7600361c	r226b: prefer unique anchors	2020-04-11 22:28:21 -04:00
Heng Li	c710c6ea48	r221: sync with hifiasm parameter ... Probably has no practical effect	2020-04-10 21:49:01 -04:00
Heng Li	22b2e1e9e1	r217: fixed a bug in LIS chaining score ... Also fall back to DP chaining more often	2020-04-10 13:25:25 -04:00
Heng Li	c3f032da37	r212: LIS chaining was not working	2020-04-09 10:43:37 -04:00
Heng Li	c41aae0630	r211: added --write-paf/--write-ec/--skip-triobin	2020-04-08 22:32:54 -04:00
Heng Li	5917aa2f36	Merge branch 'chain-tune' into merge2	2020-04-05 12:07:13 -04:00
Heng Li	f0c53e9948	r192: estimate buffer memory	2020-04-05 11:17:12 -04:00
chhylp123	ac3fcc339a	for purge_dup	2020-04-05 11:10:56 -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	483ceb852c	r179: replace one qsort() with ks_introsort()	2020-04-02 10:34:43 -04:00
Heng Li	7776dee103	r178: speedup chaining	2020-04-02 09:30:23 -04:00
Heng Li	878fe943c3	r177: combine the hifiasm and minimap2 heuristics	2020-04-01 23:07:42 -04:00
Heng Li	b7e5d1c4d3	r176: enabled the minimap2 chaining heuristic	2020-04-01 22:06:14 -04:00
Heng Li	8dbb4140bd	removed k_mer_pos_list_alloc	2020-03-27 11:27:36 -04:00
Heng Li	293f4b6b58	to replace get_new_candidates(); UNFINISHED!	2020-03-27 11:21:08 -04:00
Heng Li	7271c106e4	reverted to the older k_mer_hit definition	2020-03-27 10:40:31 -04:00
Heng Li	4aa4ebaf96	more unused code	2020-03-26 17:57:39 -04:00
Heng Li	814a3705e2	removed a few other unused functions	2020-03-26 16:33:28 -04:00
Heng Li	79bc553da6	removed hifiasm hash table index	2020-03-26 16:10:01 -04:00
Heng Li	59a9d62df9	NOT WORKING!!! backup only	2020-03-24 00:44:56 -04:00
Heng Li	3a27d104c6	replaced khash with khashl	2020-03-23 10:21:46 -04:00
Haoyu Cheng	4ac9907e49	clean code	2019-12-26 02:26:24 -05:00
Haoyu Cheng	06556e4a9b	backup without bundaries processing	2019-12-17 16:58:20 -05:00
Haoyu Cheng	f1cde019a9	for break points at chr11	2019-12-12 00:31:24 -05:00
Haoyu Cheng	09603432e5	fix bugs for overlaps of different length	2019-12-09 17:07:11 -05:00
Haoyu Cheng	ada03ea388	final DP-based assembly	2019-11-13 20:18:11 -05:00
Haoyu Cheng	d5327fe9ee	phasing	2019-09-02 10:30:14 -04:00
Haoyu Cheng	3c0c201cdf	improve speed	2019-08-26 02:22:20 -04:00
Haoyu Cheng	f508762557	resure alignment	2019-07-12 10:18:25 -04:00
Haoyu Cheng	4eddb02dbd	prefilter	2019-07-09 15:11:04 -04:00
Haoyu Cheng	1892b4d2db	prefilter	2019-07-08 01:06:36 -04:00
Haoyu Cheng	87873d6323	edit distance based error correction	2019-07-07 03:44:59 -04:00
Haoyu Cheng	b553f3ac5e	POA	2019-07-01 09:08:25 -04:00
Haoyu Cheng	30161f1544	overlap	2019-06-23 23:28:28 -04:00
Haoyu Cheng	e3924b5c08	Change stupid merge function	2019-05-19 05:02:28 -04:00
Haoyu Cheng	63509bcb7f	Accelerate overlap merge	2019-05-18 11:36:42 -04:00
Haoyu Cheng	ddd96d8456	Merge overlap	2019-05-18 01:03:24 -04:00
Haoyu Cheng	7cebaf271b	Fix bug	2019-05-17 00:52:10 -04:00
Haoyu Cheng	17553e0a42	S/L index&reads	2019-05-16 21:14:50 -04:00
Haoyu Cheng	45355a1103	Update position hash table	2019-05-14 17:02:03 -04:00
Haoyu Cheng	df18b5af76	Update modimers	2019-05-12 04:03:54 -04:00
Haoyu Cheng	9302fc6058	Finish multiple thread counting	2019-05-12 02:16:20 -04:00