@@ -18,7 +18,7 @@ setMethod("gsnap", c("character", "character_OR_NULL", "GsnapParam"),

             if (!is.null(input_b) && length(input_a) != length(input_b))

               stop("If 'input_b' is non-NULL, it must have the same length",

                    " as 'input_a'")

-            if (any(is.na(input_a)) || any(is.na(input_b)))

+            if (anyNA(input_a) || anyNA(input_b))

               stop("'input_a' and 'input_b' must not contain NA's")

             if (length(input_a) > 1L) {

                 args <- list(params, consolidate, ...)

@@ -21,9 +21,10 @@ setMethod("gsnap", c("character", "character_OR_NULL", "GsnapParam"),

             if (any(is.na(input_a)) || any(is.na(input_b)))

               stop("'input_a' and 'input_b' must not contain NA's")

             if (length(input_a) > 1L) {

-              return(GsnapOutputList(mapply(gsnap, input_a, input_b,

-                                            MoreArgs = list(params, output,

-                                              consolidate, ...))))

+                args <- list(params, consolidate, ...)

+                return(GsnapOutputList(mapply(gsnap, input_a, input_b,

+                                              output=output,

+                                              MoreArgs = args)))

             }

             output_dir <- dirname(output)

@@ -9,7 +9,7 @@

 setGeneric("gsnap", function(input_a, input_b = NULL, params, ...)

            standardGeneric("gsnap"))

-setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

+setMethod("gsnap", c("character", "character_OR_NULL", "GsnapParam"),

           function(input_a, input_b, params,

                    output = file.path(getwd(),

                      file_path_sans_ext(basename(input_a), TRUE)),

@@ -125,6 +125,10 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

   mode <- match.arg(mode)

   quality_protocol <- match.arg(quality_protocol)

   filter_chastity <- match.arg(filter_chastity)

+

+  if (version) {

+      .redirect <- ">/dev/null"

+  }

 ### TODO: if input_a is NULL, or split_output and .redirect are NULL:

 ###       return a pipe()

@@ -11,12 +11,15 @@ setGeneric("gsnap", function(input_a, input_b = NULL, params, ...)

 setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

           function(input_a, input_b, params,

-                   output = file_path_sans_ext(input_a, TRUE),

+                   output = file.path(getwd(),

+                     file_path_sans_ext(basename(input_a), TRUE)),

                    consolidate = TRUE, ...)

           {

             if (!is.null(input_b) && length(input_a) != length(input_b))

               stop("If 'input_b' is non-NULL, it must have the same length",

                    " as 'input_a'")

+            if (any(is.na(input_a)) || any(is.na(input_b)))

+              stop("'input_a' and 'input_b' must not contain NA's")

             if (length(input_a) > 1L) {

               return(GsnapOutputList(mapply(gsnap, input_a, input_b,

                                             MoreArgs = list(params, output,

@@ -30,7 +33,7 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

             params <- initialize(params, ...)

             params_list <- as.list(params)

             if (gsnap_split_output(params)) {

-              params_list$split_output <- basename(output)

+              params_list$split_output <- output

               output_path <- output_dir

             } else {

               output_path <- paste0(output, ".sam")

@@ -14,6 +14,15 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

                    output = file_path_sans_ext(input_a, TRUE),

                    consolidate = TRUE, ...)

           {

+            if (!is.null(input_b) && length(input_a) != length(input_b))

+              stop("If 'input_b' is non-NULL, it must have the same length",

+                   " as 'input_a'")

+            if (length(input_a) > 1L) {

+              return(GsnapOutputList(mapply(gsnap, input_a, input_b,

+                                            MoreArgs = list(params, output,

+                                              consolidate, ...))))

+            }

+            

             output_dir <- dirname(output)

             if (!file.exists(output_dir))

               dir.create(output_dir, recursive = TRUE)

@@ -21,7 +21,7 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

             params <- initialize(params, ...)

             params_list <- as.list(params)

             if (gsnap_split_output(params)) {

-              params_list$split_output <- output

+              params_list$split_output <- basename(output)

               output_path <- output_dir

             } else {

               output_path <- paste0(output, ".sam")

@@ -124,8 +124,10 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

 }

 .system_gsnap <- function(command) {

-  command <- paste(command, "2>&1")

-  output <- .system(command, intern = TRUE)

+  stderr <- tempfile("gsnap-stderr", fileext = "log")

+  command <- paste(command, "2>", stderr)

+  .system(command)

+  output <- readLines(stderr)

   if (!gsnapSucceeded(command, output))

     stop("Execution of gsnap failed, command-line: '", command,

          "'; last output line: '", tail(output, 1), "'")

@@ -51,7 +51,8 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

 ### Low-level interface

 ###

-.gsnap <- function(db, dir = NULL, part = NULL, input_buffer_size = 1000L,

+.gsnap <- function(db = NULL, dir = NULL, part = NULL,

+                   input_buffer_size = 1000L,

                    barcode_length = 0L,

                    orientation = c("FR", "RF", "FF"),

                    fastq_id_start = NULL, fastq_id_end = NULL,

@@ -107,7 +108,6 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

   if (!is.null(problems))

     stop("validation failed:\n  ", paste(problems, collapse = "\n  "))  

-  ##TODO: figure out how to do this programmatically

   orientation <- match.arg(orientation)

   batch <- match.arg(batch)

   mode <- match.arg(mode)

@@ -116,7 +116,26 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

 ### TODO: if input_a is NULL, or split_output and .redirect are NULL:

 ###       return a pipe()

-  .system(commandLine("gsnap"), intern = version)

+  .system_gsnap(commandLine("gsnap"))

+}

+

+..gsnap <- function(args, path = NULL) {

+  .system_gsnap(.commandLine("gsnap", args, path))

+}

+

+.system_gsnap <- function(command) {

+  command <- paste(command, "2>&1")

+  output <- .system(command, intern = TRUE)

+  if (!gsnapSucceeded(command, output))

+    stop("Execution of gsnap failed, command-line: '", command,

+         "'; last output line: '", tail(output, 1), "'")

+  else output

+}

+

+gsnapSucceeded <- function(command, output) {

+  if (!grepl("--version", command))

+    any(grepl("^Processed \\d+ queries", output))

+  else TRUE

 }

 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

@@ -198,10 +217,11 @@ setValidity("GsnapParam", .valid_GsnapParam)

 ###

 gsnapVersion <- function() {

-  version_text <- sub("GSNAP version (.*?) ", "\\1", .gsnap(version = TRUE))

+  output <- .gsnap(version = TRUE)

+  version_text <- sub("GSNAP version (.*?) .*", "\\1", output[1])

   parseGsnapVersion(version_text)

 }

 parseGsnapVersion <- function(x) {

-  as.POSIXlt(x, format = "%m-%d-%Y")

+  as.POSIXlt(x, format = "%Y-%m-%d")

 }

@@ -41,7 +41,7 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

             gsnap_output <- GsnapOutput(path = output_path,

                                         version = gsnapVersion(),

                                         param = params)

-            asBam(gsnap_output)

+            gsnap_output <- asBam(gsnap_output)

             if (consolidate)

               consolidate(gsnap_output)

             return(gsnap_output)

@@ -12,7 +12,7 @@ setGeneric("gsnap", function(input_a, input_b = NULL, params, ...)

 setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

           function(input_a, input_b, params,

                    output = file_path_sans_ext(input_a, TRUE),

-                   consolidate = TRUE, indexDestination=TRUE, ...)

+                   consolidate = TRUE, ...)

           {

             output_dir <- dirname(output)

             if (!file.exists(output_dir))

@@ -41,7 +41,7 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

             gsnap_output <- GsnapOutput(path = output_path,

                                         version = gsnapVersion(),

                                         param = params)

-            asBam(gsnap_output, indexDestination=indexDestination)

+            asBam(gsnap_output)

             if (consolidate)

               consolidate(gsnap_output)

             return(gsnap_output)

@@ -12,7 +12,7 @@ setGeneric("gsnap", function(input_a, input_b = NULL, params, ...)

 setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

           function(input_a, input_b, params,

                    output = file_path_sans_ext(input_a, TRUE),

-                   consolidate = TRUE, ...)

+                   consolidate = TRUE, indexDestination=TRUE, ...)

           {

             output_dir <- dirname(output)

             if (!file.exists(output_dir))

@@ -41,7 +41,7 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

             gsnap_output <- GsnapOutput(path = output_path,

                                         version = gsnapVersion(),

                                         param = params)

-            asBam(gsnap_output)

+            asBam(gsnap_output, indexDestination=indexDestination)

             if (consolidate)

               consolidate(gsnap_output)

             return(gsnap_output)

@@ -38,20 +38,13 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

                          c(list(.input_a = input_a, .input_b = input_b,

                                 format = "sam"),

                            params_list))

-            ##users can provide a function to the "gmapRSysCall"

-            ##option. If this has happened, the return value of .gsnap

-            ##(and consequently .system) is returned instead of a

-            ##GsnapOutput object

-            if (is.null(getOption("gmapRSysCall"))) {

-              gsnap_output <- GsnapOutput(path = output_path,

-                                          version = gsnapVersion(),

-                                          param = params)

-              asBam(gsnap_output)

-              if (consolidate)

-                consolidate(gsnap_output)

-              res <- gsnap_output

-            }

-            return(res)

+            gsnap_output <- GsnapOutput(path = output_path,

+                                        version = gsnapVersion(),

+                                        param = params)

+            asBam(gsnap_output)

+            if (consolidate)

+              consolidate(gsnap_output)

+            return(gsnap_output)

           })

 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

@@ -82,7 +82,7 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

                    gmap_mode = "pairsearch,terminal,improve",

                    trigger_score_for_gmap = 5L, max_gmap_pairsearch = 3L,

                    max_gmap_improvement = 3L, microexon_spliceprob = 0.90,

-                   novelsplicing = FALSE, splicingdir = NULL,

+                   novelsplicing = 0L, splicingdir = NULL,

                    use_splicing = NULL, ambig_splice_noclip = FALSE,

                    localsplicedist = 200000L,

                    local_splice_penalty = 0L, distant_splice_penalty = 3L,

@@ -34,17 +34,24 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

               }

             }

-            do.call(.gsnap,

-                    c(list(.input_a = input_a, .input_b = input_b,

-                           format = "sam"),

-                      params_list))

-            gsnap_output <- GsnapOutput(path = output_path,

-                                        version = gsnapVersion(),

-                                        param = params)

-            asBam(gsnap_output)

-            if (consolidate)

-              consolidate(gsnap_output)

-            gsnap_output

+            res <- do.call(.gsnap,

+                         c(list(.input_a = input_a, .input_b = input_b,

+                                format = "sam"),

+                           params_list))

+            ##users can provide a function to the "gmapRSysCall"

+            ##option. If this has happened, the return value of .gsnap

+            ##(and consequently .system) is returned instead of a

+            ##GsnapOutput object

+            if (is.null(getOption("gmapRSysCall"))) {

+              gsnap_output <- GsnapOutput(path = output_path,

+                                          version = gsnapVersion(),

+                                          param = params)

+              asBam(gsnap_output)

+              if (consolidate)

+                consolidate(gsnap_output)

+              res <- gsnap_output

+            }

+            return(res)

           })

 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

@@ -24,8 +24,14 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

               params_list$split_output <- output

               output_path <- output_dir

             } else {

-              output_path <- paste0("> ", output, ".sam")

-              params_list$.redirect <- output_path

+              output_path <- paste0(output, ".sam")

+              params_list$.redirect <- paste(">", output_path)

+            }

+

+            if (is.null(params_list$gunzip)) {

+              if (file_ext(input_a) == "gz" && file_ext(input_b) == "gz") {

+                params_list$gunzip <- TRUE

+              }

             }

             do.call(.gsnap,

@@ -65,7 +71,7 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

                    mode = c("standard", "cmet-stranded", "cmet-nonstranded",

                      "atoi-stranded", "atoi-nonstranded"),

                    tallydir = NULL, use_tally = NULL,

-                   use_runlength = NULL, nthreads = NULL,

+                   use_runlength = NULL, nthreads = 1L,

                    gmap_mode = "pairsearch,terminal,improve",

                    trigger_score_for_gmap = 5L, max_gmap_pairsearch = 3L,

                    max_gmap_improvement = 3L, microexon_spliceprob = 0.90,

@@ -28,8 +28,10 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

               params_list$.redirect <- output_path

             }

-            do.call(.gsnap, c(.input_a = input_a, .input_b = input_b,

-                              format = "sam", params_list))

+            do.call(.gsnap,

+                    c(list(.input_a = input_a, .input_b = input_b,

+                           format = "sam"),

+                      params_list))

             gsnap_output <- GsnapOutput(path = output_path,

                                         version = gsnapVersion(),

                                         param = params)

@@ -104,6 +104,7 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

   batch <- match.arg(batch)

   mode <- match.arg(mode)

   quality_protocol <- match.arg(quality_protocol)

+  filter_chastity <- match.arg(filter_chastity)

 ### TODO: if input_a is NULL, or split_output and .redirect are NULL:

 ###       return a pipe()

@@ -44,26 +44,39 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

 ###

 .gsnap <- function(db, dir = NULL, part = NULL, input_buffer_size = 1000L,

-                   barcode_length = 0L, pc_linefeeds = FALSE,

-                   orientation = c("FR", "RF", "FF"), gunzip = FALSE,

+                   barcode_length = 0L,

+                   orientation = c("FR", "RF", "FF"),

+                   fastq_id_start = NULL, fastq_id_end = NULL,

+                   filter_chastity = c("off", "either", "both"),

+                   gunzip = FALSE,

                    batch = c("2", "0", "1", "3", "4"), max_mismatches = NULL,

                    query_unk_mismatch = 0L, genome_unk_mismatch = 1L,

+                   terminal_threshold = 2L,

                    indel_penalty = 2L,

                    indel_endlength = 4L, max_middle_insertions = 9L,

                    max_middle_deletions = 30L, max_end_insertions = 3L,

                    max_end_deletions = 6L, suboptimal_levels = 0L,

                    adapter_string = NULL,

-                   trim_mismatch_score = -3L, snpsdir = NULL, use_snps = NULL,

+                   trim_mismatch_score = -3L, trim_indel_score = -4L,

+                   snpsdir = NULL, use_snps = NULL,

                    cmetdir = NULL, atoidir = NULL,

-                   mode = c("standard", "cmet", "atoi"),

-                   tallydir = NULL, use_tally = NULL, nthreads = NULL,

-                   novelsplicing = FALSE, splicing = NULL,

-                   novel_doublesplices = FALSE, localsplicedist = 200000L,

+                   mode = c("standard", "cmet-stranded", "cmet-nonstranded",

+                     "atoi-stranded", "atoi-nonstranded"),

+                   tallydir = NULL, use_tally = NULL,

+                   use_runlength = NULL, nthreads = NULL,

+                   gmap_mode = "pairsearch,terminal,improve",

+                   trigger_score_for_gmap = 5L, max_gmap_pairsearch = 3L,

+                   max_gmap_improvement = 3L, microexon_spliceprob = 0.90,

+                   novelsplicing = FALSE, splicingdir = NULL,

+                   use_splicing = NULL, ambig_splice_noclip = FALSE,

+                   localsplicedist = 200000L,

                    local_splice_penalty = 0L, distant_splice_penalty = 3L,

                    distant_splice_endlength = 16L,

                    shortend_splice_endlength = 2L,

+                   distant_splice_identity = 0.95,

+                   antistranded_penalty = 0L, merge_distant_samechr = FALSE,

                    pairmax_dna = 1000L,

-                   pairmax_rna = 200000L, pairexpect = 200L,

+                   pairmax_rna = 200000L, pairexpect = 200L, pairdev = 25L,

                    quality_protocol = c("sanger", "illumina"),

                    quality_zero_score = 33L, quality_print_shift = 0L,

                    mapq_unique_score = NULL, npaths = 100L,

@@ -71,9 +84,12 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

                    show_rediff = FALSE, clip_overlap = FALSE,

                    print_snps = FALSE, failsonly = FALSE,

                    nofails = FALSE, fails_as_input = FALSE,

-                   format = NULL, split_output = NULL, no_sam_headers = FALSE,

+                   format = NULL, split_output = NULL,

+                   output_buffer_size = 1000L,

+                   no_sam_headers = FALSE,

                    sam_headers_batch = NULL, read_group_id = NULL,

-                   read_group_name = NULL, version = FALSE,

+                   read_group_name = NULL, read_group_library = NULL,

+                   read_group_platform = NULL, version = FALSE,

                    .input_a = NULL, .input_b = NULL,

                    .redirect = NULL ## e.g., > gsnap.sam

                    )

@@ -14,20 +14,24 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

                    output = file_path_sans_ext(input_a, TRUE),

                    consolidate = TRUE, ...)

           {

+            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 {

-              params_list$.redirect <- paste0("> ", output, ".sam")

+              output_path <- paste0("> ", output, ".sam")

+              params_list$.redirect <- output_path

             }

-            output_dir <- dirname(output)

-            if (!file.exists(output_dir))

-              dir.create(output_dir, recursive = TRUE)

             do.call(.gsnap, c(.input_a = input_a, .input_b = input_b,

                               format = "sam", params_list))

-            gsnap_output <- GsnapOutput(path = output_dir, version = gsnapVersion(),

+            gsnap_output <- GsnapOutput(path = output_path,

+                                        version = gsnapVersion(),

                                         param = params)

             asBam(gsnap_output)

             if (consolidate)

@@ -71,8 +75,8 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

                    sam_headers_batch = NULL, read_group_id = NULL,

                    read_group_name = NULL, version = FALSE,

                    .input_a = NULL, .input_b = NULL,

-                   .redirect = NULL, ## e.g., > gsnap.sam

-                   extra = NULL)

+                   .redirect = NULL ## e.g., > gsnap.sam

+                   )

 {

   formals <- formals(sys.function())

   problems <- do.call(c, lapply(names(formals), .valid_gmap_parameter, formals))

@@ -84,8 +88,6 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

   batch <- match.arg(batch)

   mode <- match.arg(mode)

   quality_protocol <- match.arg(quality_protocol)

-    

-  if (identical(extra, list())) extra <- NULL

 ### TODO: if input_a is NULL, or split_output and .redirect are NULL:

 ###       return a pipe()

new file mode 100644

@@ -0,0 +1,180 @@

+### =========================================================================

+### gsnap command

+### -------------------------------------------------------------------------

+

+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

+### High-level interface

+###

+

+setGeneric("gsnap", function(input_a, input_b = NULL, params, ...)

+           standardGeneric("gsnap"))

+

+setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

+          function(input_a, input_b, params,

+                   output = file_path_sans_ext(input_a, TRUE),

+                   consolidate = TRUE, ...)

+          {

+            params <- initialize(params, ...)

+            params_list <- as.list(params)

+            if (gsnap_split_output(params)) {

+              params_list$split_output <- output

+            } else {

+              params_list$.redirect <- paste0("> ", output, ".sam")

+            }

+            output_dir <- dirname(output)

+            if (!file.exists(output_dir))

+              dir.create(output_dir, recursive = TRUE)

+            

+            do.call(.gsnap, c(.input_a = input_a, .input_b = input_b,

+                              format = "sam", params_list))

+            gsnap_output <- GsnapOutput(path = output_dir, version = gsnapVersion(),

+                                        param = params)

+            asBam(gsnap_output)

+            if (consolidate)

+              consolidate(gsnap_output)

+            gsnap_output

+          })

+

+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

+### Low-level interface

+###

+

+.gsnap <- function(db, dir = NULL, part = NULL, input_buffer_size = 1000L,

+                   barcode_length = 0L, pc_linefeeds = FALSE,

+                   orientation = c("FR", "RF", "FF"), gunzip = FALSE,

+                   batch = c("2", "0", "1", "3", "4"), max_mismatches = NULL,

+                   query_unk_mismatch = 0L, genome_unk_mismatch = 1L,

+                   indel_penalty = 2L,

+                   indel_endlength = 4L, max_middle_insertions = 9L,

+                   max_middle_deletions = 30L, max_end_insertions = 3L,

+                   max_end_deletions = 6L, suboptimal_levels = 0L,

+                   adapter_string = NULL,

+                   trim_mismatch_score = -3L, snpsdir = NULL, use_snps = NULL,

+                   cmetdir = NULL, atoidir = NULL,

+                   mode = c("standard", "cmet", "atoi"),

+                   tallydir = NULL, use_tally = NULL, nthreads = NULL,

+                   novelsplicing = FALSE, splicing = NULL,

+                   novel_doublesplices = FALSE, localsplicedist = 200000L,

+                   local_splice_penalty = 0L, distant_splice_penalty = 3L,

+                   distant_splice_endlength = 16L,

+                   shortend_splice_endlength = 2L,

+                   pairmax_dna = 1000L,

+                   pairmax_rna = 200000L, pairexpect = 200L,

+                   quality_protocol = c("sanger", "illumina"),

+                   quality_zero_score = 33L, quality_print_shift = 0L,

+                   mapq_unique_score = NULL, npaths = 100L,

+                   quiet_if_excessive = FALSE, ordered = FALSE,

+                   show_rediff = FALSE, clip_overlap = FALSE,

+                   print_snps = FALSE, failsonly = FALSE,

+                   nofails = FALSE, fails_as_input = FALSE,

+                   format = NULL, split_output = NULL, no_sam_headers = FALSE,

+                   sam_headers_batch = NULL, read_group_id = NULL,

+                   read_group_name = NULL, version = FALSE,

+                   .input_a = NULL, .input_b = NULL,

+                   .redirect = NULL, ## e.g., > gsnap.sam

+                   extra = NULL)

+{

+  formals <- formals(sys.function())

+  problems <- do.call(c, lapply(names(formals), .valid_gmap_parameter, formals))

+  if (!is.null(problems))

+    stop("validation failed:\n  ", paste(problems, collapse = "\n  "))  

+

+  ##TODO: figure out how to do this programmatically

+  orientation <- match.arg(orientation)

+  batch <- match.arg(batch)

+  mode <- match.arg(mode)

+  quality_protocol <- match.arg(quality_protocol)

+    

+  if (identical(extra, list())) extra <- NULL

+  

+### TODO: if input_a is NULL, or split_output and .redirect are NULL:

+###       return a pipe()

+  .system(commandLine("gsnap"), intern = version)

+}

+

+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

+### Validity Checking

+###

+

+.valid_GsnapParam_part <- function(x) {

+  ## validate the part string (i/n)

+}

+.valid_GsnapParam_batch <- function(x) {

+  ## one of 0, 1, 2, 3, 4

+}

+.valid_GsnapParam_max_mismatches <- function(x) {

+  ## non-negative number or NULL

+}

+.valid_GsnapParam_suboptimal_levels <- function(x) {

+  ## non-negative number or NULL

+}

+.valid_GsnapParam_use_snps <- function(x) {

+  ## a file that exists (not sure)

+}

+.valid_GsnapParam_mode <- function(x) {

+  ## one of standard, cmet, atoi

+}

+.valid_GsnapParam_nthreads <- function(x) {

+  ## positive number

+}

+.valid_GsnapParam_novelsplicing <- function(x) {

+  ## TRUE or FALSE

+}

+.valid_GsnapParam_splicing <- function(x) {

+  ## a file that exists (not sure) or NULL

+}

+.valid_GsnapParam_npaths <- function(x) {

+  ## positive number

+}

+.valid_GsnapParam_quiet_if_excessive <- function(x) {

+  ## TRUE or FALSE

+}

+.valid_GsnapParam_nofails <- function(x) {

+  ## TRUE or FALSE

+}

+.valid_GsnapParam_format <- function(x) {

+  ## sam or NULL (this is a low-level check!)

+}

+.valid_GsnapParam_split_output <- function(x) {

+  ## single string or NULL

+}

+.valid_GsnapParam_read_group_id <- function(x) {

+  ## single string (any character constraints?) or NULL

+}

+.valid_GsnapParam_read_group_name  <- function(x) {

+  ## single string or NULL

+}

+

+.valid_gmap_parameter <- function(name, params) {

+  res <- TRUE ##if we're not validating the param, assume it is good

+

+  validatorName <- paste(".valid_GsnapParam_", name, sep = "")

+  if (exists(validatorName)) {

+    validator <- get(validatorName)

+    res <- validator(params)

+  } else {

+    res <- NULL

+  }

+

+  return(res)

+}

+

+.valid_GsnapParam <- function(object) {

+  x <- as.list(object) # converts to low-level parameter list

+  do.call(c, lapply(names(x), .valid_gmap_parameter, x))

+}

+

+setValidity("GsnapParam", .valid_GsnapParam)

+

+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

+### Utilities

+###

+

+gsnapVersion <- function() {

+  version_text <- sub("GSNAP version (.*?) ", "\\1", .gsnap(version = TRUE))

+  parseGsnapVersion(version_text)

+}

+

+parseGsnapVersion <- function(x) {

+  as.POSIXlt(x, format = "%m-%d-%Y")

+}