@@ -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: 0.99.17

+Version: 0.99.18

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

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

          GenomicFeatures, Biostrings, VariantAnnotation, tools, Biobase

@@ -43,4 +43,5 @@ Collate: GmapBamReader-class.R

          makeGmapGenomePackage.R

          TP53Genome.R

          utils.R

-         

+	 asSystemCall.R

+         

\ No newline at end of file

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

 import(IRanges)

 import(GenomicRanges)

 import(parallel)

-import(LungCancerLines)

 importFrom(Biostrings, getSeq, read.DNAStringSet)

 importFrom(GenomicRanges, genome, seqinfo)

 importMethodsFrom(GenomicRanges, seqnames, strand)

new file mode 100644

@@ -0,0 +1,11 @@

+##written to get the string of the system call rather than having the

+##system call actually executed. Initial motivation was for unit

+##testing.

+asSystemCall <- function(x) {

+  expr <- substitute(x)

+  options(systemCallMode = TRUE)

+  on.exit(options(systemCallMode = FALSE))

+  error <- tryCatch(eval(expr, parent.frame()),

+                         error = function(e) return(e))

+  error$systemCall

+}

@@ -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)

           })

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

@@ -100,15 +100,16 @@ commandLine <- function(binary = "gsnap",

 ## at some point, mxbay want to customize this

 .system <- function(...) {

-  sysopt <- getOption("gmapRSysCall")

-  

-  if (is.null(sysopt)) {

-    res <- system(...)

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

-    res <- sysopt(...)

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

+    options(systemCallMode = FALSE)

+  }

+

+  sysCallModeStatus <- getOption("systemCallMode")

+  if (sysCallModeStatus == TRUE) {

+    error <- simpleError("system command")

+    error$systemCall <- as.character(as.list(...))

+    stop(error)

   } else {

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

+    system(...)

   }

-  

-  return(res)

 }