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Commit b8648abd authored by nina.marthe_ird.fr's avatar nina.marthe_ird.fr
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corrected requirements for option -pav

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...@@ -33,8 +33,8 @@ To choose where the annotations will be transfered, use these options: ...@@ -33,8 +33,8 @@ To choose where the annotations will be transfered, use these options:
Additionnal files that give informations about the transfer can be obtained with these options : Additionnal files that give informations about the transfer can be obtained with these options :
- ```-aln``` or ```--alignment``` : outputs the alignments of the annotated features in the source genome and in a target genome. - ```-aln``` or ```--alignment``` : outputs the alignments of the annotated features in the source genome and in a target genome.
- ```-var``` or ```--variation``` : outputs the detail of the variations between the features in the source genome and in the target genome. - ```-var``` or ```--variation``` : outputs the detail of the variations between the features in the source genome and in the target genome.
- ```-pav``` or ```--pav_matrix``` : outputs a presence-absence variation matrix to recapitulate the annotation transfers. Requires at least one option among ```-ann```, ```-aln``` and ```-var```. - ```-pav``` or ```--pav_matrix``` : outputs a presence-absence variation matrix to recapitulate the annotation transfers. Requires the option ```-ann/--annotation```.
<!-- could change the -pav requirements --> <!-- could change the -pav requirements to one among ann,var,aln, or no requirement-->
You can filter the annotations you transfer with these options : You can filter the annotations you transfer with these options :
- ```-cov``` or ```--coverage``` : specify the minimum requested coverage percentage between the original feature and the feature found in the target genome. Default is 80. - ```-cov``` or ```--coverage``` : specify the minimum requested coverage percentage between the original feature and the feature found in the target genome. Default is 80.
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