### =========================================================================
 ### gmap command
 ### -------------------------------------------------------------------------
 
 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 ### High-level interface
 ###
 

 setGeneric("gmap", function(input, params, ...) standardGeneric("gmap"))
 
 setMethod("gmap", c("ANY", "GmapParam"),
           function(input, params, ...) {
               tmpfile <- tempfile()
               export(input, tmpfile, format="fasta")
               input <- tmpfile
               callGeneric()
           })
 
 setMethod("gmap", c("FastaFile", "GmapParam"),
           function(input, params, ...) {
               input <- path(input)
               callGeneric()
           })
 
 setMethod("gmap", c("character", "GmapParam"),
           function(input, params,
                    output = file.path(getwd(),
                        file_path_sans_ext(basename(input), TRUE)), ...)
               {
                   if (any(is.na(input)))
                       stop("'input' must not contain NA's")
                   if (length(input) > 1L) {
                       return(GmapOutputList(mapply(gmap, input,
                                                    MoreArgs =
                                                        list(params, output,
                                                             ...))))
                   }
                   
                   output_dir <- dirname(output)
                   if (!file.exists(output_dir))
                       dir.create(output_dir, recursive = TRUE)
 
                   params <- initialize(params, ...)
                   params_list <- as.list(params)
                   if (gsnap_split_output(params)) {
                       params_list$split_output <- output
                       output_path <- output_dir
                   } else {
                       output_path <- paste0(output, ".",

                                             formatToExt(params_list$format))

                       params_list$.redirect <- paste(">", output_path)
                   }
 
                   res <- do.call(.gmap,
                                  c(list(.input = input), params_list))
                   gmap_output<- GmapOutput(path = output_path,
                                            version = gmapVersion(),
                                            param = params)
 
                   if (params_list$format %in% c("samse", "sampe")) {
                       gmap_output <- asBam(gmap_output)
                   }
                   gmap_output
               })
 

 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 ### Low-level interface
 ###

 
 .gmap <- function(db = NULL, dir = NULL,
                   kmer = NULL, basesize = NULL, sampling = NULL,
                   genomefull = FALSE, gseg = NULL,
                   selfalign = FALSE, pairalign = FALSE,
                   part = NULL, input_buffer_size = 1000L,
                   batch = c("0", "1", "2", "3", "4", "5"),
                   expand_offsets = FALSE, nosplicing = FALSE,
                   min_intronlength = 9L, intronlength = 1000000L,
                   localsplicedist = 2000000L, totallength = 2400000L,
                   chimera_margin = 40L, no_chimeras = FALSE,
                   nthreads = NULL, chrsubsetfile = NULL,
                   direction = c("auto", "sense_force", "antisense_force",
                       "sense_filter", "antisense_filter"),
                   trimendexons = 12L, canonical_mode = c("1", "0", "2"),
                   cross_species = FALSE, allow_close_indels = c("1", "0", "2"),
                   microexon_spliceprob = 0.90, cmetdir = NULL, atoidir = NULL,
                   mode = c("standard", "cmet-stranded", "cmet-nonstranded",
                       "atoi-stranded", "atoi-nonstranded"),
                   prunelevel = c("0", "1", "2", "3"),
                   format = NULL, npaths = 5L, quiet_if_excessive = FALSE,
                   suboptimal_score = NULL, ordered = FALSE, md5 = FALSE,
                   chimera_overlap = FALSE, failsonly = FALSE, nofails = FALSE,
                   fails_as_input = FALSE, snpsdir = NULL, use_snps = NULL,
                   split_output = NULL, append_output = FALSE,
                   output_buffer_size = 1000L, fulllength = FALSE,
                   cdsstart = NULL, truncate = FALSE, tolerant = FALSE,
                   no_sam_headers = FALSE, sam_use_0M = FALSE,
                   force_xs_dir = FALSE, md_lowercase_snp = FALSE,
                   read_group_id = NULL, read_group_name = NULL,
                   read_group_library = NULL, read_group_platform = NULL,
                   quality_protocol = c("sanger", "illumina"),
                   quality_print_shift = 0L, mapdir = NULL, map = NULL,
                   mapexons = FALSE, mapboth = FALSE, version = FALSE,
                   .input = NULL, .redirect = NULL)
 {
     formals <- formals(sys.function())
 
     expand_offsets <- as.integer(expand_offsets)
     batch <- match.arg(batch)
     direction <- match.arg(direction)
     canonical_mode <- match.arg(canonical_mode)
     allow_close_indels <- match.arg(allow_close_indels)
     mode <- match.arg(mode)
     prunelevel <- match.arg(prunelevel)
     quality_protocol <- match.arg(quality_protocol)
     
     if (version) {
         .redirect <- ">/dev/null"
     }
 
 ### TODO: if input_a is NULL, or split_output and .redirect are NULL:
 ###       return a pipe()
     .system_gsnap(commandLine("gmap"))
 }
 
 ..gmap <- function(args, path = NULL) {
     .system_gsnap(.commandLine("gmap", args, path))
 }
 
 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 ### Utilities
 ###
 
 gmapVersion <- function() {
     output <- .gmap(version = TRUE)
     version_text <- sub("GMAP version (.*?) .*", "\\1", output[1])
     parseGsnapVersion(version_text)
 }