def _run_args(args):
ds = ConsensusReadSet(args.ccsxml, strict=True)
orig_uuid = ds.uuid
ds.consolidate("reads.bam", useTmp=False)
bam_res = ds.externalResources[0]
if args.zmws_json:
bam_res._setSubResByMetaType("PacBio.FileTypes.json", args.zmws_json)
if args.report_ccs_processing:
bam_res._setSubResByMetaType("PacBio.FileTypes.JsonReport",
args.report_ccs_processing)
ds.uuid = orig_uuid
ds.write("final.consensusreadset.xml")
with open("reads.fofn", "wt") as fofn:
fofn.write(os.path.abspath("reads.bam"))
return 0
