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Ignore quotes in read_csv calls #75

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Ignore quotes in read_csv calls #75

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bbimber
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@bbimber bbimber commented Jan 11, 2025

The input alignment results can have single quotes within a field, such as a quality string. This PR tells read_csv to ignore quote characters, as described here:

https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.read_csv.html

This explicitly tells pandas.read_csv to skip quotes, since some fields have internal single-quotes
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bbimber commented Jan 11, 2025

Note, this also seems to work and might be better than what I propose in the PR, since it doesnt assume line endings:

d = pd.read_csv(fn, sep='\t', quoting=csv.QUOTE_NONE, engine = 'python')

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