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torognes / swarm

A robust and fast clustering method for amplicon-based studies
GNU Affero General Public License v3.0
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bug in -w output when using the -a option #106

Closed frederic-mahe closed 7 years ago

frederic-mahe commented 7 years ago

The fasta file of cluster representatives (-w) is not correct when using the -a option to append abundance values to amplicons missing one.

OUTPUT=$(mktemp)
printf ">s1\nT\n" | swarm -a 1 -w "${OUTPUT}" &> /dev/null
cat "${OUTPUT}"
rm "${OUTPUT}"

The identifier of the amplicon (s1) is missing, and only the abundance value is reported:

>_1
t
torognes commented 7 years ago

Fixed.