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Author	SHA1	Message	Date
Heng Li	4badf2fcbf	avoid wasted memory allocation for backtrack	2017-08-08 11:29:46 -04:00
Heng Li	0137d0dfab	command lines used for read simulation	2017-08-07 13:41:40 -04:00
Heng Li	5b10667967	sim-eval.js to support mason2 read names and SAM	2017-08-07 13:28:33 -04:00
Heng Li	bd1541dce1	renamed simulation-related scripts	2017-08-07 13:26:25 -04:00
Heng Li	1597f2b030	convert mason2 SAM to fastq	2017-08-07 12:45:34 -04:00
Heng Li	ce927d2aee	Merge branch 'master' into dev	2017-08-07 12:44:07 -04:00
Heng Li	8c2917b391	Added citation.	2017-08-06 21:30:47 -04:00
Heng Li	9fcf8b6315	added basic travis CI	2017-08-04 15:33:40 -04:00
Heng Li	3217178d4a	fixed k8 download page	2017-08-04 14:53:00 -04:00
Heng Li	b40598fa91	added paf2aln.js example	2017-08-04 14:51:33 -04:00
Heng Li	269b8661b9	minor clarification	2017-08-04 14:49:25 -04:00
Heng Li	890d7bbd5b	added README for misc scripts	2017-08-04 14:46:31 -04:00
Heng Li	1aca0d5098	copied sam2paf.js here for completeness	2017-08-04 14:44:37 -04:00
Heng Li	68d99f0edb	Merge branch 'cs-tag' into dev	2017-08-04 14:31:46 -04:00
Heng Li	fd66ab5413	blast-like output working	2017-08-04 14:31:21 -04:00
Heng Li	71f82759af	convert paf to maf	2017-08-04 13:05:46 -04:00
Heng Li	648cdd8a3b	minor wording changes	2017-08-04 10:21:10 -04:00
Heng Li	7e231cfd3a	minor wording improvement	2017-08-03 21:28:01 -04:00
Heng Li	95d3c30ae3	rephrasing a bit to avoid the apparent TeX bug ... Several hours sank into this. Damned...	2017-08-03 20:19:00 -04:00
Heng Li	f57fd8c790	added one transition phrase ... as there are no subsubsections now	2017-08-03 18:01:48 -04:00
Heng Li	c70b20ee6d	removed subsubsection ... TeX Live 2016 doesn't work with section and content on the same line.	2017-08-03 17:58:36 -04:00
Heng Li	e8d00a8c8c	removed trailing ^M	2017-08-03 17:20:43 -04:00
Heng Li	ed4efd77bc	minor modifications ... I will submit this version arXiv. There is definitely room for improvement, but as a semi-formal technical report, it should be good for now.	2017-08-03 12:47:36 -04:00
Heng Li	295874ea30	spell check	2017-08-03 12:17:58 -04:00
Heng Li	9ec5f51afb	the first draft	2017-08-03 12:12:55 -04:00
Heng Li	28ab4d1f72	backup	2017-08-02 22:59:58 -04:00
Heng Li	6c9390b54a	backup	2017-08-02 19:52:31 -04:00
Heng Li	9306299e4d	added benchmark results	2017-08-01 15:12:49 -04:00
Heng Li	0c563e1868	Merge branch 'dev' into tex	2017-08-01 13:53:16 -04:00
Heng Li	8b1e36c609	minor tweaks to the evaluation script	2017-08-01 13:52:29 -04:00
Heng Li	d933a263d7	backup	2017-08-01 13:29:02 -04:00
Heng Li	7542b4b40a	Makefile for TeX	2017-08-01 10:42:33 -04:00
Heng Li	d6181de844	added tech notes	2017-08-01 10:38:33 -04:00
Heng Li	12cea727b8	r238: bugfix to cs - rev sequence not complemented	2017-08-01 10:33:21 -04:00
Heng Li	cd105b47f2	r237: fixed a bug in outputting cs:Z	2017-07-31 14:49:39 -04:00
Heng Li	35f232c3fa	r236: in cs tag, output differences in lowercase ... for easy eyeballing	2017-07-31 12:17:48 -04:00
Heng Li	4c0713ee14	r235: optionally output tag cs in PAF ... cs encodes the query, the reference sequence and CIGAR.	2017-07-31 12:06:49 -04:00
Heng Li	46de0fbdad	Merge pull request #8 from rikuu/master ... fix self-comparison in index parameter override check	2017-07-30 15:10:29 -04:00
Riku Walve	9e09c1ae72	fix self-comparison in index parameter override check	2017-07-30 21:46:25 +03:00
Heng Li	d8d4d29b68	Release minimap2-2.0rc1-r232 v2.0rc1	2017-07-30 14:32:40 -04:00
Heng Li	e51dfd0330	added NEWS	2017-07-30 14:20:03 -04:00
Heng Li	1f78e1ee53	r230: code formatting changes only	2017-07-30 12:31:40 -04:00
Heng Li	5934d68772	r229: a new way to prevent out-of-band backtrack	2017-07-29 23:52:30 -04:00
Heng Li	fa99d28d34	r228: reduced unnecessary INV alignment	2017-07-29 20:21:53 -04:00
Heng Li	d08b7a0c51	r227: use local alignment for INV alignment	2017-07-29 17:40:53 -04:00
Heng Li	da3db3c095	r226: only try inv alignment for primary	2017-07-29 14:09:35 -04:00
Heng Li	783ead6f47	r225: removed a debugging line	2017-07-29 13:21:38 -04:00
Heng Li	19d6ec885e	r224: inversion alignment around Z-drop break	2017-07-29 13:09:10 -04:00
Heng Li	120bebc290	ake	2017-07-29 11:01:49 -04:00
Heng Li	5e3eecd6d4	r222: no effective changes	2017-07-29 10:31:46 -04:00