r537: model the next base to GT/AG

mirror of https://github.com/lh3/minimap2.git synced 2026-10-07 21:08:12 +08:00

[PMID:18688272] shows that the base following GT tends to be A or G (i.e. R) in
both human and yeast, and that the base preceeding AG tends to be C or T (i.e.
Y). In the new model, we pay no cost to GTr..yAG, but we pay half of the cost
if there is no r or y. This improves the junction accuracy when mapping to
human and mouse and decreases the accuacy when mapping to SIRV. My guess is
that SIRV does not honor this trend. Need to investigate in future.

Also in this commit, --cost-non-gt-ag is aliased to -C. The default is changed
to 9 instead of 5. I also added --splice-flank to enable the above model. This
may become the default once I confirm my hypothesis on SIRV.

This commit is contained in:

Heng Li

2017-10-28 00:25:01 -04:00

parent afc2f2e84b

commit 79b0caca95

7 changed files with 32 additions and 20 deletions

									
										minimap.h
									
		+1
		
												View File
												
				@@ -23,6 +23,7 @@

				#define MM_F_2_IO_THREADS  0x8000

				#define MM_F_LONG_CIGAR    0x10000

				#define MM_F_INDEPEND_SEG  0x20000

				#define MM_F_SPLICE_FLANK  0x40000

				#define MM_IDX_MAGIC   "MMI\2"