diff --git a/minimap2.html b/minimap2.html
index 813a96f..b371583 100644
--- a/minimap2.html
+++ b/minimap2.html
@@ -219,9 +219,15 @@ ignore minimizers occuring more than
-U INT1[,INT2] | |
Lower and upper bounds of k-mer occurrences [10,1000000]. The final k-mer occurrence threshold is
max{INT1, min{INT2, -f}}. This option prevents excessively small or large
--f estimated from the input reference. It deprecates
+-f estimated from the input reference. Available since r1034 and deprecating
--min-occ-floor in earlier versions of minimap2.
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+|
+--q-occ-frac FLOAT |
| |
+Discard a query minimizer if its occurrence is higher than
+FLOAT fraction of query minimizers and than the reference occurrence threshold
+[0.01]. Set 0 to disable. Available since r1105.
+ |
|
-e INT |
Sample a high-frequency minimizer every
@@ -492,6 +498,11 @@ alignment.
Skip alignment if the DP matrix size is above
NUM. Set 0 to disable [100m].
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+|
+--cap-kalloc NUM |
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+Free thread-local kalloc memory reservoir if after the alignment the size of the reservoir above
+NUM. Set 0 to disable [0].
+ |
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@@ -653,7 +664,7 @@ Long assembly to reference mapping
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splice |
Long-read spliced alignment
-(-k15 -w5 --splice -g2k -G200k -A1 -B2 -O2,32 -E1,0 -C9 -z200 -ub --junc-bonus=9 --cap-sw-mem=0 --splice-flank=yes). In the splice mode, 1) long deletions are taken as introns and represented as
+(-k15 -w5 --splice -g2k -G200k -A1 -B2 -O2,32 -E1,0 -b0 -C9 -z200 -ub --junc-bonus=9 --cap-sw-mem=0 --splice-flank=yes). In the splice mode, 1) long deletions are taken as introns and represented as
the
‘N’ CIGAR operator; 2) long insertions are disabled; 3) deletion and insertion gap
costs are different during chaining; 4) the computation of the
@@ -666,7 +677,7 @@ Long-read splice alignment for PacBio CCS reads
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sr |
Short single-end reads without splicing
-(-k21 -w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -r100 -p.5 -N20 -f1000,5000 -n2 -m20 -s40 -g100 -2K50m --heap-sort=yes --secondary=no). |
+(-k21 -w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -b0 -r100 -p.5 -N20 -f1000,5000 -n2 -m20 -s40 -g100 -2K50m --heap-sort=yes --secondary=no).
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ava-pb |
PacBio CLR all-vs-all overlap mapping
@@ -837,4 +848,4 @@ non-SSE2/NEON support, but it would make minimap2 slower by several times.
miniasm(1), minimap(1), bwa(1).
- | minimap2-2.21 (r1071) | minimap2 (1) | 6 July 2021 |
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