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pebbles's Issues

Previews in countess

Currently there is no mechanism to process a limited number of reads for generating a preview.
This means the countess interface generates a preview from a full run, making it inefficient and unresponsive.

Combining multiple files does not work

Traceback (most recent call last):
File "/Users/wakefield/PycharmProjects/CountESS/countess/core/pipeline.py", line 53, in execute
self.result = self.plugin.run(input_data, logger, row_limit)
File "/Users/wakefield/PycharmProjects/CountESS/countess/core/plugins.py", line 176, in run
df = self.load_files(logger, row_limit)
File "/Users/wakefield/PycharmProjects/CountESS/countess/core/plugins.py", line 301, in load_files
callback(num_files, num_files + 1, "Combining")
NameError: name 'callback' is not defined

Handle absence of MD tags better

If reads don't have MD tags an error is logged to the console.
This probably should raise a more visible error in the GUI as it will result in no variants being found

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