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load_mocat_sample - missing pair.2 fails, missing pair.1 succeeds #120

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unode opened this issue Sep 10, 2019 · 5 comments
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load_mocat_sample - missing pair.2 fails, missing pair.1 succeeds #120

unode opened this issue Sep 10, 2019 · 5 comments
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@unode
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@unode unode commented Sep 10, 2019

If the folder contains:

sample
├── sample.pair.1.fq.bz2
└── sample.single.fq.bz2

using load_mocat_sample() fails with the error:

Cannot find match for file: sample/sample.pair.1.fq.bz2

However in the case of:

sample
├── sample.pair.2.fq.bz2
└── sample.single.fq.bz2

it succeeds with:

(...) load_mocat_sample found single-end sample 'sample/sample.pair.2.fq.bz2'
(...) load_mocat_sample found single-end sample 'sample/sample.single.fq.bz2'

Should we also fail here due to an unpaired pair.2 and be symmetrical with the pair.1 case?

@luispedro

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@luispedro luispedro commented Sep 11, 2019

It's a strange corner case, but I think it could be a good thing to at least issue a warning.

@unode

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@unode unode commented Sep 11, 2019

Would you oppose making it into an error instead of warning? Rationale being that if it matches pair.X but there's no pair.Y something unexpected happened and the warning might go by unnoticed.

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@luispedro luispedro commented Sep 11, 2019

No objection. Never silently screw up is one of the principles that we try to adhere to and I can see how a warning may be too tame.

@unode

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@unode unode commented Sep 11, 2019

I'll make it into an error then as soon as I find the time. Thanks for the feedback.

@unode unode self-assigned this Sep 11, 2019
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@unode unode commented Oct 18, 2019

As of 68188ed an error will be raised if pair.2 exists but pair.1 doesn't.

@unode unode closed this Oct 18, 2019
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