Update prediction_tools.py#169
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Issue: the default behavior of maxATAC predict is to generate bigWig files with 10 zoom levels (i.e., pre-computed summary statistics that enable quick zooming of bigWig files). This is extremely memory-intensive, but lower values of this parameter result in delayed loading of files in e.g., IGV.
Solution:
Added a new argument ("max_zooms") for the maxATAC predict function in parser.py, which defaults to 5. This will allow users to specify how many zoom levels they wish to retain in the final bigWig file (0-10). I successfully tested the argument for the above functions by specifying all possible values of --max_zooms in my function call.
Also added code to convert values in the array used to generate the bigWig file from FP32 to FP16 values in prediction_tools.py. This code was also successfully tested.
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Issue: the default behavior of maxATAC
predictis to generate bigWig files with 10 zoom levels (i.e., pre-computed summary statistics that enable quick zooming of bigWig files). This is extremely memory-intensive, but lower values of this parameter result in delayed loading of files in e.g., IGV.Solution:
predictfunction in parser.py, which defaults to 5. The argument serves as an input for thewrite_predictions_to_bigwigfunction in prediction_tools.py. This will allow users to specify how many zoom levels they wish to retain in the final bigWig file (0-10). I successfully tested the argument for the above functions by specifying three values of --max_zooms (1, 5, and 10) in my function call.