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-a SEQUENCE... should not anchor #329

marcelm opened this issue Aug 30, 2018 · 0 comments


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commented Aug 30, 2018

  • Using -a ADAPTER... is alternative syntax for specifying a 5' adapter and is currently equivalent to -g ^ADAPTER. The -a option should not do implicit anchoring and instead it should be equivalent to -g ADAPTER. Since this feature is underdocumented (if at all), backwards compatibility is likely not an issue.

  • However, in addition the same should apply for linked adapters. -a ADAPTER1...ADAPTER2 currently automatically anchores the first adapter, but it should not do this. This is backwards incompatible.

marcelm added a commit that referenced this issue Feb 27, 2019

@marcelm marcelm closed this in 9939462 Mar 6, 2019

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