#!/usr/bin/env Rscript
suppressPackageStartupMessages(library(rtracklayer))

gff_cleanup = function(gff){
  ## remove overlapin annotation track - assign new annot
  gff_disjoin = disjoin(gff, with.revmap=TRUE)
  ## append annotation:
  gff_names = mclapply(as.list(gff_disjoin$revmap), FUN = function(x)gff$Name[x], mc.cores = 8)
  gff_strands = mclapply(as.list(gff_disjoin$revmap), FUN = function(x)strand(gff[x]), mc.cores = 8)
  new_annot = sapply(sapply(gff_names, unique), paste, collapse="|")
  strand_attribute = sapply(sapply(gff_strands, unique), paste, collapse="|")
  gff_disjoin$strands=strand_attribute
  gff_disjoin$source="RM"
  gff_disjoin$type="repeat"
  gff_disjoin$score=NA
  gff_disjoin$phase=NA
  gff_disjoin$Name=new_annot
  gff_disjoin$revmap=NULL
  return(gff_disjoin)
}
infile = commandArgs(T)[1]
outfile = commandArgs(T)[2]

## infile = "./test_data/raw_rm.out"

rm_out = read.table(infile, as.is=TRUE, sep="", skip = 2, fill=TRUE, header=FALSE)

gff = GRanges(seqnames = rm_out$V5, ranges = IRanges(start = rm_out$V6, end=rm_out$V7))

# repeat class after # symbol - syntax 1
gff$Name=rm_out$V11

## is repeat type is specifies by double underscore:
## then rm_out$V11 is unspecified
if (any(rm_out$V11 == "Unspecified")){
  ## set Name from prefix
  ## TODO
  inc = rm_out$V11 == "Unspecified"
  Name = gsub("__.+","",rm_out$V10)
  # chanche Usnpsecified to new name
  gff$Name[inc] = Name
}


## join neighbors with the same annotation, disregard strand!
result <- unlist(reduce(split(gff, gff$Name)))
result$Name <- names(result)

## TODO
## identify conflicting annotation, replace by LCA but keep origin list of classifications

gff_out = sortSeqlevels(result)
gff_out = sort(gff_out)
gff_out$type = "repeat_region"
gff_out$source = "RepeatMasker_parsed"
gff_out$ID=paste0(gff_out$Name, "_", seq_along(gff_out$Name))
export(gff_out,  format = "gff3", con=outfile)