r537: model the next base to GT/AG

mirror of https://github.com/lh3/minimap2.git synced 2026-10-08 02:58:12 +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

									
										ksw2.h
									
		+1
		
												View File
												
				@@ -14,6 +14,7 @@

				#define KSW_EZ_REV_CIGAR   0x80 // reverse CIGAR in the output

				#define KSW_EZ_SPLICE_FOR  0x100

				#define KSW_EZ_SPLICE_REV  0x200

				#define KSW_EZ_SPLICE_FLANK 0x400

				#ifdef __cplusplus

				extern "C" {