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Adding files to do with SAM format #218

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Adding files to do with SAM format #218

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sophiemathias
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Issue #199

sophiemathias and others added 18 commits September 5, 2014 14:38
@sophiemathias
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Contains debug print statements at the moment

@terrycojones
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I had a look at your pull request & can tell you why the tests are failing. It's not your fault... the input file is being opened & read twice by your code, but the test setup only provides the data once (which is consumed by checkSAMfile) so when you come to read the "file" it looks like it's empty. I'll see if I can figure out how to get around this - I've hit it before. The mock library is unfortunately complicated to use in this case - or seems to be to me.

@sophiemathias
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I was starting to come to the conclusion that it was something to do with the test framework. Thanks for helping to clear this up!

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@sophiemathias @terrycojones