Add on the fly demux and speed up barcode matching. #1649
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Hmm I can't seem to get these tests to fail locally. @gbggrant would you mind testing as well? |
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@gbggrant I think it makes the most sense to concentrate on the other PRs right now and then once they are merged come back to this one after a rebase since it will be changed significantly by the others. |
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@gbggrant This one is a little bit more substantive but it is ready for review. |
jessicaway
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gbggrant
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assigned jacarey and unassigned gbggrant, jacarey, jessicaway and nikellepetrillo
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Even without on the fly demux, this saves me a full day when demultiplexing a single NovaSeq lane. Would love to be able to use an official release with this feature! |
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@jacarey is this ready to go? |
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@gbggrant Just updated to latest. Once tests are green it is good to go. |
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Description
The purpose of this PR is twofold:
IlluminaBasecallsToSamandIlluminaBasecallsToFastqSample input parameters are parsed in a central place now which can parse any one of the following types of files:
A single barcode extractor is used for all 3 programs to do demultiplexing and metrics collection/output.
Test data was changed for the following reason:
The old test data was using static barcode files that were created before
HAMMINGwas introduced. In order to minimize the number of test data files needed the barcode files were regenerated usingHAMMINGand the test data was updated to reflect this change.Checklist (never delete this)
Never delete this, it is our record that procedure was followed. If you find that for whatever reason one of the checklist points doesn't apply to your PR, you can leave it unchecked but please add an explanation below.
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