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If ePrimer3 does not generate primers, the pipeline hangs #22

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widdowquinn opened this issue Mar 28, 2018 · 0 comments
Open

If ePrimer3 does not generate primers, the pipeline hangs #22

widdowquinn opened this issue Mar 28, 2018 · 0 comments
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@widdowquinn
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widdowquinn commented Mar 28, 2018

While looking at P. capsici data, the eprimer3 step can generate .eprimer3 files with no contents. This is not currently detected as a problem by pdp, and trying to process an empty file hangs the pipeline.

Proposed solution: detect empty .eprimer3 files and report an error.

Another option: also require that sequences being stitched are longer than the proposed length of primers, and add an option to --fix_sequences.

@widdowquinn widdowquinn self-assigned this Mar 28, 2018
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