Filtered BED file is never used

[watronfire]

The lastest commit adds a section to the variant calling script which concatenates bcftool filtered-masked positions with depth-masked bed file. However the file produced by this section ($DIR/04_assembly/$SAMPLENAME.allmask.bed) is never used.

I assume this file is supposed as the masking parameter for bcftools consensus but it currently uses just the BED file generated by BCFtools alone.