71 Commits

Author	SHA1	Message	Date
chhylp123	3a1a3750e9	Merge branch 'master' of https://github.com/chhylp123/Long_read_assembly	2020-11-16 01:49:07 -05:00
chhylp123	d87314a07e	resolve conflict	2020-11-16 01:44:12 -05:00
Heng Li	eddb8173da	added --min-hist-cnt for #49	2020-10-26 16:28:30 -04:00
chhylp123	0cc02035c5	HiC full index	2020-10-26 11:01:48 -04:00
chhylp123	b2b4624cea	rerelease v0.13	2020-10-22 14:24:59 -04:00
chhylp123	91d4915da7	release v0.13	2020-10-21 21:57:43 -04:00
chhylp123	03cf0d475c	save bfore multiple overlaps	2020-08-23 08:46:33 -04:00
chhylp123	ef5ba0cc2c	update help/man	2020-07-31 21:32:02 -04:00
chhylp123	ace34ae2b8	for high-het and coverage	2020-07-28 13:07:35 -04:00
Heng Li	1e4d67ee64	r288: reorganized command line help messages	2020-07-19 13:43:30 -04:00
Heng Li	ff4ef89fe3	r287: fixed the INT32_MAX compiling error	2020-07-19 11:22:23 -04:00
chhylp123	952471657f	change max coverage of pri-range	2020-07-18 17:40:58 -04:00
chhylp123	fda858f9e7	update coverage	2020-07-13 22:34:26 -04:00
chhylp123	c01b593d7c	using coverage	2020-07-12 16:03:01 -04:00
chhylp123	a25c37ed89	update k-mer peaks	2020-07-07 13:20:25 -04:00
chhylp123	71f6c93d58	add options	2020-06-08 17:51:36 -04:00
Heng Li	eddbc61952	r254: added --ex-list and --ex-iter	2020-06-03 20:46:34 -04:00
Heng Li	3364a29b87	r249: make max overlap error rate CLI options	2020-05-06 01:16:50 -04:00
chhylp123	7f6725ead3	expose purge_dups	2020-04-18 00:45:47 -04:00
Heng Li	85c57fd087	r246: made purge_dups optional for trio binning	2020-04-15 23:57:18 -04:00
Heng Li	a06ee39433	r244: use 3 rounds of error correction by default	2020-04-13 19:51:15 -04:00
Heng Li	cc166c8ff5	r235: clarified option -f	2020-04-12 19:42:02 -04:00
Heng Li	4d7600361c	r226b: prefer unique anchors	2020-04-11 22:28:21 -04:00
Heng Li	15591c9038	improve documentation	2020-04-10 11:04:35 -04:00
Heng Li	f32bfc904a	r215: prepare for list-based binning	2020-04-10 00:12:19 -04:00
Heng Li	7a35bd7fcc	r213: renamed trio binning output files	2020-04-09 20:40:01 -04:00
Heng Li	c41aae0630	r211: added --write-paf/--write-ec/--skip-triobin	2020-04-08 22:32:54 -04:00
Heng Li	adbc65feda	r201: automatically adjust -N	2020-04-05 22:43:01 -04:00
Heng Li	0f1994fc1f	r198: made VERBOSE_GFA a CL option --dbg-gfa	2020-04-05 13:01:03 -04:00
Heng Li	f0c53e9948	r192: estimate buffer memory	2020-04-05 11:17:12 -04:00
Heng Li	8c27dbb52f	r191: changed the default to -N400 -k51 -w51	2020-04-04 12:55:19 -04:00
Heng Li	dbe66d259d	r189: print statistics	2020-04-04 00:14:53 -04:00
Heng Li	18b69f1a72	r187: reversed round in clear_opt()	2020-04-03 22:19:55 -04:00
Heng Li	ffba3ce0ef	r182: explain -N	2020-04-03 10:42:09 -04:00
Heng Li	968b4caef9	r181: limit the max number of chains	2020-04-02 21:55:00 -04:00
Heng Li	e75b93ae12	r175: start versioning	2020-03-28 11:52:14 -04:00
Heng Li	1d4f34a36c	changed the default -D from 7 to 5	2020-03-28 11:43:44 -04:00
Heng Li	5e16483b43	option to skip k-mer filtering	2020-03-27 22:32:39 -04:00
Heng Li	19648873b9	exposed mz_win and high_factor to CLI	2020-03-27 21:39:57 -04:00
Heng Li	e116f6e09d	position table; unfinished	2020-03-25 19:17:07 -04:00
Heng Li	3e897560c4	minimizer filtering apparently works	2020-03-25 00:38:13 -04:00
Heng Li	f70257c260	support HPC k-mer	2020-03-24 19:58:21 -04:00
Heng Li	64edb06e08	NOT WORKING!!! added all k-mer counter	2020-03-24 12:29:46 -04:00
Heng Li	59a9d62df9	NOT WORKING!!! backup only	2020-03-24 00:44:56 -04:00
chhylp123	3c1d3cf6a1	disable debug	2020-03-23 00:25:20 -04:00
chhylp123	670bd10093	update man	2020-03-22 18:01:04 -04:00
chhylp123	90e290636a	code clean	2020-03-22 17:06:36 -04:00
chhylp123	c72d419711	for hifiasm 3.0	2020-03-22 16:54:32 -04:00
chhylp123	6246132702	update for 0.2.0	2020-02-07 14:52:14 -05:00
chhylp123	c63ce670f7	improved N50	2020-01-14 10:59:51 -05:00