20 Commits

Author	SHA1	Message	Date
Heng Li	3c997ca016	r337: support CPU dispatch for gcc-4.8+ ... using __builtin_cpu_supports()	2017-09-03 14:29:49 -04:00
Heng Li	993a2bb521	r301: separate introns from deletions ... When an intron is adjacent to a deletion, the old code count both as introns, which lead to an inaccurate exon boundary.	2017-08-18 15:31:15 +08:00
Heng Li	43506edbc5	backup: preliminary boundary alignment	2017-08-12 23:10:14 -04:00
Heng Li	61eef0575c	separate out spliced alignment; not right yet	2017-08-12 18:54:32 -04:00
Heng Li	163fa36ee6	r281: don't open long gaps on query	2017-08-10 15:04:59 -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	d08b7a0c51	r227: use local alignment for INV alignment	2017-07-29 17:40:53 -04:00
Heng Li	71c988f6ab	r188: renamed bseq* to mm_bseq* ... to avoid naming collisions between minimap2 and bwa/fermi-lite/etc	2017-07-19 09:26:46 -04:00
Heng Li	cc554aee43	r159: use two-piece gap penalty	2017-07-08 10:26:00 -04:00
Heng Li	d274e1b743	backup	2017-06-29 12:58:52 -04:00
Heng Li	5e202afb5f	fixed invalid backtracking, a temporary solution	2017-06-28 18:17:57 -04:00
Heng Li	42283ef10c	r87: fixed a bug in ksw2	2017-06-27 13:29:48 -04:00
Heng Li	c02ff4662c	r85: two-round z-drop	2017-06-27 10:36:24 -04:00
Heng Li	4fea3d778a	backup	2017-06-23 18:57:00 -04:00
Heng Li	c6d5dea314	replace with newer versions	2017-06-22 12:30:45 -04:00
Heng Li	fbfd4a3eff	to replace	2017-06-22 12:30:22 -04:00
Heng Li	fe8327500f	implemented SSE version; NOT working yet ... need to take a rest. Debugging is going to be tough.	2017-06-16 21:35:51 -04:00
Heng Li	7d33acbccc	diagonal global almost working ... one shot, though gaps not left-aligned at the boundary	2017-06-16 12:17:23 -04:00
Heng Li	78fe89d1ab	revert to fixed band	2017-06-14 14:22:23 -04:00
Heng Li	d3f17b1e05	updated ksw	2017-06-11 16:51:01 -04:00