r508: use two I/O threads for mapping

-x sr applies this option by default
This commit is contained in:
Heng Li
2017-10-12 14:56:01 -04:00
parent 2801ed9b4b
commit 7c555f9b7e
4 changed files with 15 additions and 6 deletions
+7 -1
View File
@@ -256,6 +256,12 @@ sequences, and uses up to
threads when mapping (the extra thread is for I/O, which is frequently idle and
takes little CPU time).
.TP
.B -2
Use two I/O threads during mapping. By default, minimap2 uses one I/O thread.
When I/O is slow (e.g. piping to gzip, or reading from a slow pipe), the I/O
thread may become the bottleneck. Apply this option to use one thread for input
and another thread for output, at the cost of increased peak RAM.
.TP
.BI -K \ NUM
Number of bases loaded into memory to process in a mini-batch [200M].
Similar to option
@@ -343,7 +349,7 @@ tag ignores introns to demote hits to pseudogenes.
Short single-end reads without splicing
.RB ( -k21
.B -w11 -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000,5000 -n2 -m20 -s40 -g200
.B -K50m --frag
.B -2K50m --frag
.BR --sr ).
.RE
.SS Miscellaneous options