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Note: I’m reworking pARP completely so that zooming in/out is actually performed on the circular display rather than in a linear representation. See the zoom_with_context branch

Using pARP

For v0.8 you’ll have to do quite a few things manually.

1. Make sure the prerequisites are in place
2. Get your datafiles into the data/ directory in the right format (see FileFormat)
3. Change the filenames in parp.rb
4. Run the script create_continuous_index.rb script to extract the first and last line number of readdepth data for each chromosome
5. Run “jruby ./parp.rb”

Prerequisites

• jruby
• ruby-processing

This Processing tool makes heavy use of Buffers. See the link for a full explanation of how these were set up.

ToDo

ZoomingCalculations