diff --git a/minimap2.html b/minimap2.html
index 75b082c..49d8648 100644
--- a/minimap2.html
+++ b/minimap2.html
@@ -260,7 +260,7 @@ Equivalent to
-p FLOAT |
Minimal secondary-to-primary score ratio to output secondary mappings [0.8].
Between two chains overlaping over half of the shorter chain (controlled by
---mask-level), the chain with a lower score is secondary to the chain with a higher score.
+-M), the chain with a lower score is secondary to the chain with a higher score.
If the ratio of the scores is below
FLOAT, the secondary chain will not be outputted or extended with DP alignment later.
This option has no effect when
@@ -289,6 +289,11 @@ Mark as secondary a chain that overlaps with a better chain by
FLOAT or more of the shorter chain [0.5]
|
|
+--hard-mask-level |
| |
+Honor option
+-M and disable a heurstic to save unmapped subsequences.
+ |
+|
--max-chain-skip INT |
| |
A heuristics that stops chaining early [50]. Minimap2 uses dynamic programming
for chaining. The time complexity is quadratic in the number of seeds. This
@@ -301,6 +306,11 @@ on chains. Set
Disable the long gap patching heuristic. When this option is applied, the
maximum alignment gap is mostly controlled by
-r. |
+|
+--lj-min-ratio FLOAT |
| |
+Fraction of query sequence length required to bridge a long gap [0.5]. A
+smaller value helps to recover longer gaps, at the cost of more false gaps.
+ |
|
--splice |
Enable the splice alignment mode.
@@ -313,6 +323,10 @@ if no good chain is found. In addition, minimap2 attempts to patch gaps between
seeds with ungapped alignment.
|
|
+--split-prefix STR |
| |
+Prefix to create temporary files. Typically used for a multi-part index.
+ |
+|
--frag=no|yes |
| |
Whether to enable the fragment mode [no]
|
@@ -394,6 +408,10 @@ How to find canonical splicing sites GT-AG -
Score bonus when alignment extends to the end of the query sequence [0].
|
+--score-N INT |
| |
+Score of a mismatch involving ambiguous bases [1].
+ |
+|
--splice-flank=yes|no |
| |
Assume the next base to a
GT donor site tends to be A/G (91% in human and 92% in mouse) and the preceding
@@ -416,6 +434,11 @@ Drop a terminal anchor if
with
--splice. It helps to avoid tiny terminal exons. [6]
|
+|
+--no-end-flt |
| |
+Don’t filter seeds towards the ends of chains before performing base-level
+alignment.
+ |
|
@@ -467,6 +490,10 @@ Output the
Output the MD tag (see the SAM spec).
|
+--eqx |
+Output =/X CIGAR operators for sequence match/mismatch.
+ |
+|
-Y |
In SAM output, use soft clipping for supplementary alignments.
|
@@ -671,6 +698,8 @@ the SAM-like typed key-value format. Minimap2 may output the following tags:
cg | Z | CIGAR string (only in PAF) |
| cs | Z | Difference string |
+
+| dv | f | Approximate per-base sequence divergence |
@@ -727,4 +756,4 @@ non-SSE2/NEON support, but it would make minimap2 slower by several times.
miniasm(1), minimap(1), bwa(1).
- | minimap2-2.10 (r761) | minimap2 (1) | 27 March 2018 |