hal2vg will automatically translate _sub_X_Y into [X-Y]. The former is what cactus-graphmap-split uses to mark subpaths in HAL (without using special characters that annoy hubs). The latter is what vg expects.
clip-vg updated to properly resolve subpath naming when splitting. Note: it is not fully handled in the bed input (so a bed file with chr1 would not be applied to a path with chr1[100-300])... but the bed logic is currently not part of the pipeline...
hal2vgwill automatically translate_sub_X_Yinto[X-Y]. The former is whatcactus-graphmap-splituses to mark subpaths in HAL (without using special characters that annoy hubs). The latter is what vg expects.clip-vgupdated to properly resolve subpath naming when splitting. Note: it is not fully handled in the bed input (so a bed file with chr1 would not be applied to a path with chr1[100-300])... but the bed logic is currently not part of the pipeline...