# should start1 and end1 be the same???


# if`index_file = TRUE`, sort, compress and index file. if FALSE, a text-like svcnv file is created --- used mainly for checking purpuses. 

bedpe_to_svcnv = function(annotated_sv, output_prefix, index_file = TRUE, 
                          overwrite_files = FALSE){
  
  # check paramters
  if(index_file){
    sort_file = TRUE
    compress_file = TRUE
  }
  
  # create the json column
  json = with(
    annotated_sv,
    gettextf('{"dt": 5, "chrB": "%s", "posB": %i, "sample": "%s", "strandA": "%s", "strandB": "%s"}',
             chrom2, start2, tumour_sample_id, strand1, strand2)
  )
  
  # create the svcnv table
  svcnv = dplyr::select(annotated_sv, chrom1, start1, end1) %>% 
    bind_cols(json = json)
  
  # write the svcnv file
  if(index_file){
    svcnv_file = tempfile(pattern = "svcnv_")
  }else{
    svcnv_file = paste0(output_prefix, ".svcnv")
    if(!overwrite_files & file.exists(svcnv_file)){
      k = gettextf("File %s already exists. Set `overwrite_files` to TRUE if you want to overwrite it.",
                   svcnv_file)
      stop(k)
    }
  }
  write.table(svcnv, svcnv_file, quote = FALSE, sep = "\t", row.names = FALSE, col.names = FALSE)
  
  if(index_file){
    # sort svcnv file
    sorted_svcnv_file = tempfile(pattern = "sorted_svcnv_")
    cmd = gettextf("sort -k1,1 -k2,2n %s > %s", svcnv_file, sorted_svcnv_file)
    system(cmd)
    unlink(svcnv_file)
    
    # compress svcnv file
    compressed_svcnv_file = paste0(output_prefix, "_sorted.svcnv.gz")
    if(!overwrite_files & file.exists(compressed_svcnv_file)){
      k = gettextf("File %s already exists. Set `overwrite_files` to TRUE if you want to overwrite it.",
                   compressed_svcnv_file)
      stop(k)
    }
    cmd = gettextf("bgzip %s", sorted_svcnv_file)
    system(cmd)
    cmd = paste0(sorted_svcnv_file, ".gz") %>% 
      gettextf("mv %s %s", ., compressed_svcnv_file)
    system(cmd)
    unlink(sorted_svcnv_file)
    
    # index svcnv file
    index_svcnv_file = sub("\\.gz$", ".tbi", compressed_svcnv_file)
    if(!overwrite_files & file.exists(index_svcnv_file)){
      k = gettextf("File %s already exists. Set `overwrite_files` to TRUE if you want to overwrite it.",
                   index_svcnv_file)
      stop(k)
    }
    cmd = gettextf("tabix -p bed %s", compressed_svcnv_file)
    system(cmd)
  }
}