fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-09-30 13:48:13 +08:00
Code Issues Packages Projects Releases Wiki Activity

r159: use two-piece gap penalty

Browse Source
This commit is contained in:
Heng Li
2017-07-08 10:26:00 -04:00
parent 9823317e8f
commit cc554aee43
9 changed files with 499 additions and 113 deletions
Download Patch File Download Diff File Expand all files Collapse all files
minimap2.1
+12 -9
View File
@@ -192,23 +192,26 @@ Long assembly to reference mapping (-k19 -w19)
.SS Alignment options
.TP 10
.BI -A \ INT
Matching score [1]
Matching score [2]
.TP
.BI -B \ INT
Mismatching penalty [2]
Mismatching penalty [4]
.TP
.BI -O \ INT
Gap open penalty [2]
.BI -O \ INT1[,INT2]
Gap open penalty [4,24]. If
.I INT2
is not specified, it is set to
.IR INT1 .
.TP
.BI -E \ INT
Gap extension penalty [1]. A gap of length
.I l
.BI -E \ INT1[,INT2]
Gap extension penalty [2,1]. A gap of length
.I k
costs
.RI {-O}+{-E}* l .
.RI min{ O1 + k * E1 , O2 + k * E2 }.
.TP
.BI -z \ INT
Break an alignment if the running score drops too quickly along the diagonal of
the DP matrix (diagonal X-drop, or Z-drop) [200]. Increasing the value improves
the DP matrix (diagonal X-drop, or Z-drop) [400]. Increasing the value improves
the contiguity of the alignment at the cost of poor alignment in the middle
(e.g. caused by a long inversion).
.TP