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r917: added --max-chain-iter to avoid worst case

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Resolves #324
This commit is contained in:
Heng Li
2019-02-27 14:41:01 -05:00
parent ccf1680aaf
commit d431dc0181
8 changed files with 20 additions and 9 deletions
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@@ -1,4 +1,4 @@
.TH minimap2 1 "5 Feburary 2019" "minimap2-2.15-dirty (r913)" "Bioinformatics tools"
.TH minimap2 1 "27 Feburary 2019" "minimap2-2.15-dirty (r917)" "Bioinformatics tools"
.SH NAME
.PP
minimap2 - mapping and alignment between collections of DNA sequences
@@ -232,13 +232,19 @@ Honor option
and disable a heurstic to save unmapped subsequences.
.TP
.BI --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
.I INT
to a large number to switch off this heurstics.
.TP
.BI --max-chain-iter \ INT
Check up to
.I INT
partial chains during chaining [5000]. This is a heuristic to avoid quadratic
time complexity in the worst case.
.TP
.B --no-long-join
Disable the long gap patching heuristic. When this option is applied, the
maximum alignment gap is mostly controlled by