16 Commits

Author	SHA1	Message	Date
Heng Li	e3d8c708ac	r1208: reverted RMQ gap coefficient ... Such that minimap2 can give the same alignment in other modes	2024-03-27 08:48:10 -04:00
Heng Li	89d4d219cd	r1206: enabled RMQ for lr:hqae ... Also fixed a bug in determining inner_dist for RMQ. It should have no effect on previous presets.	2024-03-20 15:29:54 -04:00
Heng Li	f51ff1abac	r1205: updated lr:hqae	2024-03-20 14:06:59 -04:00
Heng Li	27b254ed6f	backup; DON'T USE!!!	2024-03-20 10:21:10 -04:00
Heng Li	f18dadb1c4	r1202: halved RMQ gap cost	2024-03-19 23:47:54 -04:00
Heng Li	c22bfe7722	r1200: added --rmq-inner and --dbg-seed-freq	2024-03-19 21:52:07 -04:00
Chris Seymour	e68d868806	use updated kalloc macros (#1051) ... * use updated kalloc macros * review * get the reference * store the reference * last one	2023-04-21 10:45:53 -04:00
Heng Li	226fd6114c	fixed a wrong comment. Resolves #997	2022-11-30 09:22:39 -05:00
Heng Li	c2f07ff2ac	r1149: implemented random open syncmer ... On the mm2-update dataset, -j8 leads to sparser k-mer selection at higher accuracy. The speed becomes a little slower. There seems a benefit but not a big one.	2022-10-21 19:07:28 -04:00
Heng Li	36942ff711	r1119: fixed a typo in the new chaining code ... Not affecting v2.23	2021-12-25 12:46:26 -05:00
Heng Li	fcaadc22b7	r1116: cut long chains at weak points	2021-11-20 19:07:44 -05:00
Heng Li	db37fc43a7	r1115: prepare for chain breaking	2021-11-20 13:42:44 -05:00
Heng Li	2546999639	dev-r1076: log gap penalty	2021-07-17 18:23:59 -04:00
Heng Li	459ce04c84	r1069: fixed a regression in comparison to v2.18 ... for PE short reads. An interesting omission. Resolves #776	2021-07-02 11:45:21 -04:00
Heng Li	e74dfd1aa9	r1054: fixed a memory leak	2021-05-26 12:32:04 -04:00
Heng Li	e81927e7a1	prepare to backport unimap/minigraph chaining	2021-05-02 18:25:49 -04:00