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bjpop / rover

Read overlap variant caller.
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Add an argument to specify the name of the coverage file #1

Closed bjpop closed 10 years ago

bjpop commented 11 years ago

At the moment the coverage file name is based on the name of the sample. The coverage file is written to the working directory from which rover is run. It would be nice to be able to specify an alternative name and place to store the coverage files.

bjpop commented 11 years ago

Rover can take multiple BAM files as input. It will generate a coverage file for each BAM file. So we cannot supply a single output name for the coverage files.

Instead we propose to add an extra optional command-line argument which specifies the directory to store the coverage files. The default behaviour should be to write them into the current working directory.

bjpop commented 10 years ago

This was addressed in acc276e7f08a1b4b0a11933aab457f7550387613