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Set default ir1p or ir2p #79

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PeteHaitch opened this issue Jun 12, 2014 · 2 comments
Closed

Set default ir1p or ir2p #79

PeteHaitch opened this issue Jun 12, 2014 · 2 comments
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@PeteHaitch
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If the user doesn't want any --ir1p or --ir2p then currently they must explicitly set it as --ir1p 0 and --ir2p 0. This isn't intuitive. Need better defaults so that if the user doesn't supply either option comethylation still works.
@PeteHaitch PeteHaitch added the bug label Jun 12, 2014
@PeteHaitch
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Relatedly, make sure that --ir1p 0 means no trimming and not trimming of the first base.

@PeteHaitch
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Needed to convert command line arguments (1-based) to internal co-ordinates (0-based).

@PeteHaitch PeteHaitch reopened this Aug 12, 2014
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@PeteHaitch