def compute_comparison(job, baseline, graph, options):
""" run vg compare between two graphs
"""
graph_index_path = index_path(graph, options)
assert os.path.exists(graph_index_path)
baseline_index_path = index_path(baseline, options)
assert os.path.exists(baseline_index_path)
out_path = comp_path(baseline, graph, options)
do_comp = options.overwrite or not os.path.exists(out_path)
if do_comp:
os.system("vg compare {} {} -t {} > {}".format(baseline, graph,
min(2, options.vg_cores),
out_path))
def compute_kmer_index(job, graph, options):
""" run vg index (if necessary) and vg compare on the input
vg indexes are just created in place, ie same dir as graph,
so need to have write permission there
"""
out_index_path = index_path(graph, options)
do_index = options.overwrite or not os.path.exists(out_index_path)
index_opts = "-s -k {} -t {}".format(options.kmer, options.vg_cores)
if options.edge_max > 0:
index_opts += " -e {}".format(options.edge_max)
if do_index:
os.system("vg index {} {}".format(index_opts, graph))
