"clean" function unmasks the genome?

[wackerk]

Hello,

We have screened and cleaned many de novo assemblies with fcs-gx. We used the cleaning command:

 cat ${FASTA} | python3 ${FCSGS_SCRIPT} --image ${IMAGE} --env-file /work/kwacker/env.txt \
        clean genome \
        --action-report ${REPORT} \
        --output ${CLEAN_OUT} \
        --contam-fasta-out ${CONTAM_OUT}

Repeats were soft-masked prior to screening, but appear to be completely unmasked in the output fasta. Is this supposed to happen? Is there a way to disable this behavior?

Thanks for your help.

[pstrope]

The output of clean genome is uppercased fasta. Currently there's no way to disable it. We may add preserving of lowercase-softmasking in the future.