test

jhavsmith · Nov 24, 2019 · e343123 · e343123
1 parent 641a911
commit e343123
Showing 1 changed file with 0 additions and 6 deletions.
diff --git a/R/functions.R b/R/functions.R
@@ -1,11 +1,6 @@
 
 #This runs the full sequence of functions below.
-<<<<<<< HEAD
-run.startmrca = function(vcf.file, rec.file, mut.rate, rec.rate = NULL, nsel = NULL, nanc = NULL, chain.length = 15000, proposal.sd = 20, nanc.post = 100, sample.ids, refsample.ids = NULL, pos, sel.allele = 1, bed.file = NULL, upper.t.limit = 2000) {
-	    recover()
-=======
 run.startmrca = function(vcf.file, rec.file, mut.rate, rec.rate = NULL, nsel = NULL, nanc = NULL, chain.length = 15000, proposal.sd = 20, nanc.post = 100, sample.ids, refsample.ids = NULL, pos, sel.allele = 1, bed.file = NULL, upper.t.limit = 2000, output.file = NULL) {
->>>>>>> 69307b34e57939e0eab894fc1065e58c8bc5d8da
         params = make.params(vcf.file, rec.file, mut.rate, rec.rate, nsel, nanc, chain.length, proposal.sd, nanc.post, sample.ids, refsample.ids, pos, sel.allele, bed.file, upper.t.limit)
         input.list = get.vcfdata.func(params)
         prep.list = prep.func(input.list,params)
@@ -46,7 +41,6 @@ make.params = function(vcf.file, rec.file, mut.rate, rec.rate, nsel, nanc, chain
 
 #This puts the genotype data from the the vcf into an R matrix format.
 get.vcfdata.func = function(params) {
-	recover()
     print("Getting data from the vcf.")
     vcf.file = params$vcf.file
     file.name = params$file.name