Boundary Error when input contains short sequences

[JMAStough]

Error description Julia stops the script with a Boundary Error and this appears to happen when the input fasta file contains sequences are too short for Julia to select 100 base chunks at the ends.

Fixing the error This issue needs to be tested with sequences of different sizes to see how small they have to be to cause the error, and then code needs to be added to check whether input sequences are long enough to avoid the error.

Using ccontigs with this issue ccontigs works fine when input sequences are at least 1kb, and the problem likely only occurs with sequences shorter than 200 bases, so if you are using this software in the meantime, you can used reformat.sh from BBMap to filter out short sequences from your input files before using ccontigs.

[Microbiology]

Thanks for flagging up! While good to fix these things, in my mind since the goal is finding circular genomes or other large elements, it’s probably not encountered often. But I could probably see other applications that might want it.