In pggb, -n is the number of haplotypes/genomes in the input dataset.
In wfmash, -n is the maximum number of mappings to consider for each homologous region identified in the input dataset. To avoid overlapping (relevant for small datasets), wfmash -n has to be set as pggb -n minus 1.
Furthermore, consensus graph generation has been disabled (due to #133 and #182 issues) and it will be for a while.
In
pggb,-nis the number of haplotypes/genomes in the input dataset. Inwfmash,-nis the maximum number of mappings to consider for each homologous region identified in the input dataset. To avoid overlapping (relevant for small datasets),wfmash -nhas to be set aspggb -nminus 1.Furthermore, consensus graph generation has been disabled (due to #133 and #182 issues) and it will be for a while.