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.
This commit is contained in:
Heng Li
2022-10-21 19:07:28 -04:00
parent cefd0d9f6c
commit c2f07ff2ac
9 changed files with 84 additions and 8 deletions
+13
View File
@@ -79,6 +79,19 @@ Minimizer k-mer length [15]
.BI -w \ INT
Minimizer window size [10]. A minimizer is the smallest k-mer
in a window of w consecutive k-mers.
.TP
.BI -j \ INT
Syncmer submer size [10]. Option
.B -j
and
.B -w
will override each: if
.B -w
is applied after
.BR -j ,
.B -j
will have no effect, and vice versa.
.TP
.B -H
Use homopolymer-compressed (HPC) minimizers. An HPC sequence is constructed by