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FOI-Bioinformatics / CanSNPer2

CanSNPer2: A toolkit for SNP-typing bacterial genomes.
GNU General Public License v3.0
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Correct for mauve error #15

Closed davve2 closed 4 years ago

davve2 commented 4 years ago

Progressive mauve that is used for alignment in the current version of CanSNPer2 does not handle genomes containing gaps "-". Implement an error function that replaces "-" with "N" in genomes that fails with exitcode 11 to allow more genomes to be processed.

davve2 commented 4 years ago

A function is implemented that replaces any gaps (-) with N and retry progressiveMauve, tested and working.