diff --git a/minimap2.html b/minimap2.html index c320acf..e521044 100644 --- a/minimap2.html +++ b/minimap2.html @@ -189,6 +189,15 @@ the index. Indexing options are fixed in the index file. When an index file is provided as the target sequences, options -H, -k, -w, -I will be effectively overridden by the options stored in the index file. + +--alt FILE +List of ALT contigs [null] + + +--alt-drop FLOAT   +Drop ALT hits by +FLOAT fraction when ranking and computing mapping quality [0.15] + @@ -291,8 +300,13 @@ Mark as secondary a chain that overlaps with a better chain by --hard-mask-level   Honor option --M and disable a heurstic to save unmapped subsequences. - +-M and disable a heurstic to save unmapped subsequences and disables +--mask-len. + +--mask-len NUM   +Keep an alignment if dropping it leaves an unaligned region on query longer than +INT [inf]. Effective without +--hard-mask-level. --max-chain-skip INT   A heuristics that stops chaining early [25]. Minimap2 uses dynamic programming @@ -308,6 +322,10 @@ Check up to time complexity in the worst case. +--chain-gap-scale FLOAT   +Scale of gap cost during chaining [1.0] + + --no-long-join   Disable the long gap patching heuristic. When this option is applied, the maximum alignment gap is mostly controlled by @@ -446,7 +464,7 @@ BED12 file can be converted from GTF/GFF3 with ‘paftools.js gff2bed anno.gt --junc-bonus INT   Score bonus for a splice donor or acceptor found in annotation (effective with ---junc-bed) [0]. +--junc-bed) [9]. --end-seed-pen INT   @@ -740,6 +758,8 @@ the SAM-like typed key-value format. Minimap2 may output the following tags: ASiDP alignment score +SAZList of other supplementary alignments + msiDP score of the max scoring segment in the alignment nniNumber of ambiguous bases in the alignment @@ -811,4 +831,4 @@ non-SSE2/NEON support, but it would make minimap2 slower by several times. miniasm(1), minimap(1), bwa(1).

-
minimap2-2.17 (r941) minimap2 (1) 4 May 2019
+
minimap2-2.18 (r1015) minimap2 (1) 9 April 2021