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View Code? Open in Web Editor NEWExtract a section of a reference genome flanking an input locus with SNPs.
Extract a section of a reference genome flanking an input locus with SNPs.
The section '6. Select only the top amplicons' is probably no longer needed, as all amplicons are carried through to the end and then limited within the final Rscript.
Removal of this section will require renaming some files and testing that it is truly not needed.
If there are instances where the alleles in the RAD tags are [A\T] instead of [A/T], or if a mistake is [A/T} instead of [A/T], it breaks the output for that locus.
Probably need to include a screen at the start of the process for the character "" or "{" or "}" to avoid these issues, to throw a warning at least, or to edit the character to the correct version.
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