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explain -M in the manpage

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Heng Li 2018-01-18 11:47:11 -05:00
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commit 0454e6be91
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@ -182,6 +182,11 @@ Maximum fragment length (aka insert size; effective with
.BR -xsr / --frag) .BR -xsr / --frag)
[800] [800]
.TP .TP
.BI -M \ FLOAT
Mark as secondary a chain that overlaps with a better chain by
.I FLOAT
or more of the shorter chain [0.5]
.TP
.BI --max-chain-skip \ INT .BI --max-chain-skip \ INT
A heuristics that stops chaining early [50]. Minimap2 uses dynamic programming A heuristics that stops chaining early [50]. Minimap2 uses dynamic programming
for chaining. The time complexity is quadratic in the number of seeds. This for chaining. The time complexity is quadratic in the number of seeds. This