@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read

     to work with GMAP and GSNAP from within R. In addition, it provides 

     methods to tally alignment results on a per-nucleotide basis using 

     the bam_tally tool.

-Version: 0.99.15

+Version: 0.99.16

 Depends: R (>= 2.15.0), methods, GenomicRanges

 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15), GenomicRanges,

          GenomicFeatures, Biostrings, VariantAnnotation, tools, Biobase

@@ -8,6 +8,7 @@ importFrom(Biobase, createPackage)

 import(IRanges)

 import(GenomicRanges)

 import(parallel)

+import(LungCancerLines)

 importFrom(Biostrings, getSeq, read.DNAStringSet)

 importFrom(GenomicRanges, genome, seqinfo)

 importMethodsFrom(GenomicRanges, seqnames, strand)

@@ -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)

           })

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

@@ -81,16 +81,34 @@ commandLine <- function(binary = "gsnap",

   on.exit(options(scipen = scipen))

   unnamedUserArgs <- sapply(userArgs[!named], as.character)

-  namedUserArgs <- paste(ifelse(nchar(names(userArgs[named])) > 1, "--", "-"),

-                            gsub("_", "-", names(userArgs[named])), sep = "")

+  ##long-form args have double dashes. Short-form args (single char)

+  ##have single dashes.

+  dashes <- ifelse(nchar(names(userArgs[named])) > 1, "--", "-")

+  namedUserArgs <- paste(dashes,

+                         gsub("_", "-", names(userArgs[named])),

+                         sep = "")

   toggle_arg <- sapply(userArgs[named], isTRUE)

   namedUserArgs[!toggle_arg] <-

     paste(namedUserArgs[!toggle_arg],

-          sapply(userArgs[named][!toggle_arg], as.character))

+          sapply(userArgs[named][!toggle_arg], as.character),

+          sep="=")

   if (!is.null(path))

     binary <- file.path(path, binary)

   paste(binary, paste(c(namedUserArgs, unnamedUserArgs), collapse = " "))

 }

 ## at some point, mxbay want to customize this

-.system <- function(...) system(...)

+.system <- function(...) {

+

+  sysopt <- getOption("gmapRSysCall")

+  

+  if (is.null(sysopt)) {

+    res <- system(...)

+  } else if (class(sysopt) == "function") {

+    res <- sysopt(...)

+  } else {

+    stop("If the gmapRSysCall option is provided, it must be a function.")

+  }

+  

+  return(res)

+}