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r1241: error out on unintended --score-N

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Resolve #1226
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Heng Li
2025-04-01 10:12:53 -04:00
parent a955b1f31d
commit e816fd071c
3 changed files with 7 additions and 2 deletions
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minimap2.1
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@@ -414,7 +414,7 @@ no attempt to match GT-AG [n]
Score bonus when alignment extends to the end of the query sequence [0].
.TP
.BI --score-N \ INT
Score of a mismatch involving ambiguous bases [1].
Penalty of a mismatch involving ambiguous bases [1].
.TP
.BI --pe-ind-chain
For paired-end short reads, perform chaining for each end independently.