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| data_calcul_position=data_new_germline[,c(1,2,2,3,4)]
colnames(data_calcul_position)=c("chrom","position","positionEnd","ref","var")
calculs_g=function(i,data_calcul_position,data_new_germline){
if (substr(data_calcul_position$var[i],1,1)=="-")
{
data_calcul_position$position[i]=data_calcul_position$position[i]+1
data_calcul_position$positionEnd[i]=data_calcul_position$positionEnd[i]+nchar(as.character(data_calcul_position$var[i]))-1
data_calcul_position$new_ref[i]= sapply(strsplit(as.character(data_calcul_position$var[i]), "-"), function(x) x[2])
data_calcul_position$new_var[i]="-"
}
else if (substr(data_calcul_position$var[i],1,1)=="+")
{
data_calcul_position$position[i]=data_calcul_position$position[i]+1
data_calcul_position$positionEnd[i]=data_calcul_position$positionEnd[i]+1
data_calcul_position$new_ref[i]="-"
data_calcul_position$new_var[i]=sapply(strsplit(as.character(data_calcul_position$var[i]), "+"), function(x) x[2])
data_new_germline$position[i]=data_calcul_position$position[i]
}
else
{
data_calcul_position$new_ref[i]=as.character(data_calcul_position$ref[i])
data_calcul_position$new_var[i]=as.character(data_calcul_position$var[i])
}
return(list(data_calcul_position,data_new_germline))
}
s_calcul_g=sapply(1:nrow(data_calcul_position), function(i) {calculs_g(i,data_calcul_position,data_new_germline)})
data_calcul_position=s_calcul_g |