gistfile1.txt

library(tidyverse)
x<-read.table("~/Desktop/ogut.map")

# OK we're missing bits on  ends
group_by(x,V1) %>% 
  summarize(end=max(V3),start=min(V3))

#spline to get them
pos.starts<-rep(0,10)
pos.ends<-c(307041717,244442276,235667834,246994605,223902240,174033170,182381542,181122637,159769782,150982314)

for(chr in  1:10){
  bob<-subset(x,x$V1==chr)
  sue=spline(x=bob$V4,y=bob$V3,xout=c(pos.starts[chr],pos.ends[chr]))$y
  start<-data.frame(chr,pos.starts[chr],sue[1])
  colnames(start)=c("V1","V4","V3")
  end<-data.frame(chr,pos.ends[chr],sue[2])
  colnames(end)=c("V1","V4","V3")
  bob<-select(bob,V1,V4,V3)
  y=rbind(start,bob,end)
  y$V3=y$V3+abs(min(y$V3))
  colnames(y)=c("chr","pos","map") 
  y<-mutate(y,cmdist=c(diff(y$map),"NA"),
            posdist=c(diff(y$pos),"NA")) %>%
    filter(cmdist!="NA") %>%
    mutate(cmdist=as.numeric(cmdist),posdist=as.numeric(posdist),rate=cmdist/posdist*1E6)%>%
    select(pos,rate,map)
  write.table(y,file=paste("~/Desktop/ogut.chr",chr,".txt",sep=""),quote=F,row.names=F,col.names=F)        
}