From 514612bda2bfb6af723b85dda4ab7ce1792c2321 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Thu, 28 Feb 2019 15:59:13 -0500 Subject: [PATCH] updated manpage to v2.16 --- minimap2.html | 41 ++++++++++++++++++++++++++++++++++++++--- 1 file changed, 38 insertions(+), 3 deletions(-) diff --git a/minimap2.html b/minimap2.html index 49d8648..b8d3251 100644 --- a/minimap2.html +++ b/minimap2.html @@ -295,13 +295,19 @@ Honor option --max-chain-skip INT   -A heuristics that stops chaining early [50]. Minimap2 uses dynamic programming +A heuristics that stops chaining early [25]. Minimap2 uses dynamic programming for chaining. The time complexity is quadratic in the number of seeds. This option makes minimap2 exits the inner loop if it repeatedly sees seeds already on chains. Set INT to a large number to switch off this heurstics. +--max-chain-iter INT   +Check up to +INT partial chains during chaining [5000]. This is a heuristic to avoid quadratic +time complexity in the worst case. + + --no-long-join   Disable the long gap patching heuristic. When this option is applied, the maximum alignment gap is mostly controlled by @@ -345,6 +351,11 @@ Only map to the reverse complement strand of the reference sequences. If yes, sort anchors with heap merge, instead of radix sort. Heap merge is faster for short reads, but slower for long reads. [no] + +--no-pairing   +Treat two reads in a pair as independent reads. The mate related fields in SAM +are still properly populated. + @@ -439,6 +450,11 @@ with Don’t filter seeds towards the ends of chains before performing base-level alignment. + +--cap-sw-mem NUM   +Skip alignment if the DP matrix size is above +NUM. Set 0 to disable [0]. + @@ -452,6 +468,11 @@ Generate CIGAR and output alignments in the SAM format. Minimap2 outputs in PAF by default. +-o FILE +Output alignments to +FILE [stdout]. + + -Q Ignore base quality in the input file. @@ -528,6 +549,16 @@ memory. --secondary=yes|no   Whether to output secondary alignments [yes] + +--max-qlen NUM   +Filter out query sequences longer than +NUM. + +--paf-no-hit   +In PAF, output unmapped queries; the strand and the reference name fields are +set to ‘*’. Warning: some paftools.js commands may not work with such output +for the moment. + --version Print version number to stdout @@ -575,7 +606,7 @@ Long assembly to reference mapping asm20 Long assembly to reference mapping -(-k19 -w10 -A1 -B6 -O6,26 -E2,1 -s200 -z200 --min-occ-floor=100). Up to 20% sequence divergence. +(-k19 -w10 -A1 -B4 -O6,26 -E2,1 -s200 -z200 --min-occ-floor=100). Up to 20% sequence divergence. ava-pb @@ -700,6 +731,10 @@ the SAM-like typed key-value format. Minimap2 may output the following tags: csZDifference string dvfApproximate per-base sequence divergence + +defGap-compressed per-base sequence divergence + +rliLength of query regions harboring repetitive seeds

@@ -756,4 +791,4 @@ non-SSE2/NEON support, but it would make minimap2 slower by several times. miniasm(1), minimap(1), bwa(1).

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minimap2-2.13 (r850) minimap2 (1) 11 October 2018
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minimap2-2.16 (r922) minimap2 (1) 28 Feburary 2019