From 3508ac98170279b04b4752a43c99f183291d0bc5 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Thu, 11 Oct 2018 13:35:09 -0400 Subject: [PATCH] updated manpage to v2.13 --- minimap2.html | 33 +++++++++++++++++++++++++++++++-- 1 file changed, 31 insertions(+), 2 deletions(-) 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: cgZCIGAR string (only in PAF) csZDifference string + +dvfApproximate 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).

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minimap2-2.10 (r761) minimap2 (1) 27 March 2018
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minimap2-2.13 (r850) minimap2 (1) 11 October 2018