Changes

res2<-conditional.rareMETALS2.single(candidate.variant.vec=c("19:42906914","19:45854819"), score.stat.file, cov.file,known.variant.vec=c("19:43995275","19:44047839","19:44084155"), maf.cutoff=0.05, no.boot =1000,

  res2<-conditional.rareMETALS2.single(candidate.variant.vec=c("19:42906914","19:45854819"), score.stat.file, cov.file,known.variant.vec=c("19:43995275","19:44047839","19:44084155"), maf.cutoff=0.05, no.boot =1000,

                             alternative = c("two.sided"), ix.gold = 1,

                             alternative = c("two.sided"), ix.gold = 1,out.digits = 4, callrate.cutoff = 0, hwe.cutoff = 0,p.value.known.variant.vec = NA, anno.known.variant.vec = NA,anno.candidate.variant.vec = NA)

                            out.digits = 4, callrate.cutoff = 0, hwe.cutoff = 0,

                            p.value.known.variant.vec = NA, anno.known.variant.vec = NA,

                            anno.candidate.variant.vec = NA)

   print(res2$res.out)

   print(res2$res.out)