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widdowquinn / find_differential_primers

Code for design of diagnostic PCR primers, and metabarcoding markers.
https://widdowquinn.github.io/find_differential_primers/
MIT License
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If ePrimer3 does not generate primers, the pipeline hangs #22

Open widdowquinn opened 6 years ago

widdowquinn commented 6 years ago

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.