68 Commits

Author	SHA1	Message	Date
chhylp123	b992a07d05	inbananced coverage	2024-04-02 10:40:11 -04:00
chhylp123	286b897881	r513	2023-02-16 00:04:06 -05:00
chhylp123	0613b18af9	r493 ->HiC/UL/Trans	2023-01-11 20:38:45 -05:00
chhylp123	3d1787e57a	ul_refine_alignment	2022-10-29 17:15:19 -04:00
chhylp123	df3e0eeaa3	read extract	2022-10-19 13:23:25 -04:00
chhylp123	1d0562ebd1	done second alignment	2022-10-09 16:59:54 -04:00
chhylp123	8a4d6a5f24	done alignemnt	2022-10-04 15:31:23 -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	a2198891e7	smaller memory requirement	2022-05-12 16:15:58 -04:00
chhylp123	0ce5a7ba5b	integration/print het sites	2022-01-17 18:29:48 -05:00
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	e774a83be2	debug mbg	2021-05-30 09:02:25 -04:00
chhylp123	0a2559e4a0	freeze-r304	2020-08-23 23:36:45 -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
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