GH1563: add defaults for some columns

[yanick]

This is for #1563

Big ⚠️ -> I am not using this package directly, so I'm likely to have made assumptions that are wrong.

This being said, the case reported in the issue is going 💥 because two columns are not present in a csv file. I'm assuming that is a valid schema of that file, and that it's reasonable to set the values of those columns to be '0' if not found.

If I'm mistaken and the csv absolutely needs to have those columns, the patch will have to be changed to politely tell the user that their format is wonky. :-)

• This comment contains a description of changes (with reason)
• CHANGELOG.md has been updated

[skanwal]

@yanick a quick comment as you mentioned you aren't using this module directly - if you've time, I think this comment can also be tackled as part of your PR to read correct read stats column from a different file Quality_Stats.csv, which is very useful metrics.

[ewels]

Many thanks for this @yanick!

I continued your PR on a bit, adding in parsing functionality for the new Quality_Metrics.csv file mentioned by @Garrett-Ng in #1563 (comment) (as suggested by @skanwal above). The module should now work with both types of output and give comparable reports, based on testing with the example data provided in #1563.

Please all give this new code a try and let me know if you hit any problems 👍🏻

Phil