##============ Sink warnings and errors to a file ==============
## use the sink() function to wrap all code within it.
##==============================================================
zz = file('warnings_and_errors.txt')
sink(zz)
sink(zz, type = 'message')

  ##============== load packages ===============================
  library(getopt)
  library(rmarkdown)
  library(htmltools)
  library(dplyr)
  library(Rsubread)
  library(DT)
  ##============================================================

  ##---------below is the code for rendering .Rmd templates-----

  ##=============STEP 1: handle command line arguments==========
  ##
  ##============================================================
  # column 1: the long flag name
  # column 2: the short flag alias. A SINGLE character string
  # column 3: argument mask
  #           0: no argument
  #           1: argument required
  #           2: argument is optional
  # column 4: date type to which the flag's argument shall be cast.
  #           possible values: logical, integer, double, complex, character.
  #-------------------------------------------------------------
  #++++++++++++++++++++ Best practice ++++++++++++++++++++++++++
  # 1. short flag alias should match the flag in the command section in the XML file.
  # 2. long flag name can be any legal R variable names
  # 3. two names in args_list can have common string but one name should not be a part of another name.
  #    for example, one name is "ECHO", if another name is "ECHO_XXX", it will cause problems.
  #+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
  args_list=list()
  ##------- 1. input data ---------------------
  args_list$e = c('echo', 'e', '1', 'logical')
  args_list$a = c('input_bam_paths', 'a', '1', 'character')
  args_list$N = c('input_bam_names', 'N', '1', 'character')
  args_list$b = c('annot_inbuilt', 'b', '1', 'character')
  args_list$c = c('annot_ext', 'c', '1', 'character')
  args_list$f = c('isGTFAnnotationFile', 'f', '1', 'logical')
  args_list$g = c('gtf_feature_type', 'g', '1', 'character')
  args_list$h = c('gtf_attr_type', 'h', '1', 'character')
  args_list$i = c('chr_aliases', 'i', '2', 'character')
  args_list$j = c('use_meta_features', 'j', '1', 'logical')
  args_list$k = c('allow_multi_overlap', 'k', '1', 'logical')
  args_list$l = c('min_overlap', 'l', '1', 'integer')
  args_list$m = c('largest_overlap', 'm', '1', 'logical')
  args_list$n = c('read_extension_5', 'n', '1', 'integer')
  args_list$o = c('read_extension_3', 'o', '1', 'integer')
  args_list$p = c('read_2_pos', 'p', '1', 'character')
  args_list$q = c('count_multi_mapping_reads', 'q', '1', 'logical')
  args_list$u = c('fraction', 'u', '1', 'logical')
  args_list$v= c('min_mqs', 'v', '1', 'integer')
  args_list$w= c('split_only', 'w', '1', 'logical')
  args_list$x= c('non_split_only', 'x', '1', 'logical')
  args_list$y= c('primary_only', 'y', '1', 'logical')
  args_list$z= c('ignore_dup', 'z', '1', 'logical')
  args_list$A= c('strand_specific', 'A', '1', 'integer')
  args_list$B= c('junc_counts', 'B', '1', 'logical')
  args_list$C= c('genome', 'C', '1', 'character')
  args_list$D= c('is_paired_end', 'D', '1', 'logical')
  args_list$E= c('require_both_ends_mapped', 'E', '1', 'logical')
  args_list$F= c('check_frag_length', 'F', '1', 'logical')
  args_list$G= c('min_frag_length', 'G', '1', 'integer')
  args_list$H= c('max_frag_length', 'H', '1', 'integer')
  args_list$I= c('count_chimeric_fragments', 'I', '1', 'logical')
  args_list$J= c('auto_sort', 'J', '1', 'logical')
  args_list$K= c('n_threads', 'K', '1', 'integer')
  args_list$L= c('max_mop', 'L', '1', 'integer')
  args_list$M= c('report_reads', 'M', '1', 'logical')
  
  ##--------2. output report and outputs --------------
  args_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
  args_list$REPORT_DIR = c('report_dir', 'd', '1', 'character')
  args_list$SINK_MESSAGE = c('sink_message', 's', '1', 'character')
  ##--------3. .Rmd templates in the tool directory ----------
  args_list$TOOL_TEMPLATE_RMD = c('tool_template_rmd', 't', '1', 'character')
  ##-----------------------------------------------------------
  opt = getopt(t(as.data.frame(args_list)))



  ##=======STEP 2: create report directory (optional)==========
  ##
  ##===========================================================
  dir.create(opt$report_dir)

  ##=STEP 3: replace placeholders in .Rmd with argument values=
  ##
  ##===========================================================
  #++ need to replace placeholders with args values one by one+
  readLines(opt$tool_template_rmd) %>%
    (function(x) {
      gsub('ECHO', opt$echo, x)
    }) %>%
    (function(x) {
      gsub('REPORT_DIR', opt$report_dir, x)
    }) %>%
    (function(x) {
      fileConn = file('tool_template.Rmd')
      writeLines(x, con=fileConn)
      close(fileConn)
    })


  ##=============STEP 4: render .Rmd templates=================
  ##
  ##===========================================================
  render('tool_template.Rmd', output_file = opt$report_html)


  ##--------end of code rendering .Rmd templates----------------
sink()
##=========== End of sinking output=============================