@@ -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: 1.1.9

+Version: 1.1.10

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

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

          GenomicFeatures, Biostrings, VariantAnnotation, tools, Biobase

@@ -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")

 }

@@ -31,7 +31,7 @@ getDefaultGmapPath <- function() {

 ## gathers command line from non-NULL args to parent frame

 commandLine <- function(binary = "gsnap",

-                        path = getOption("gmap.path", getDefaultGmapPath()))

+                        path = NULL)

 {

   ##get values of arguments of function that called this function

   parentFormals <- formals(sys.function(sys.parent()))

@@ -94,13 +94,18 @@ commandLine <- function(binary = "gsnap",

   ##long-form args separate arg name and value with "=". Not strictly

   ##necessary since getopts handles them, but has caused confusion so

   ##adding

-  namedUserArgs[nchar(dashes) > 1] <- sub(" ", "=", namedUserArgs[nchar(dashes) > 1])

-  if (!is.null(path))

-    binary <- file.path(path, binary)

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

+  namedUserArgs[nchar(dashes) > 1] <-

+    sub(" ", "=", namedUserArgs[nchar(dashes) > 1])

+  .commandLine(binary, namedUserArgs, unnamedUserArgs, path = path)

+}

+

+.commandLine <- function(binary, ..., path = NULL) {

+  if (is.null(path))

+    path <- getOption("gmap.path", getDefaultGmapPath())

+  arg.string <- paste(c(...), collapse = " ")

+  paste(file.path(path, binary), arg.string)

 }

-## at some point, mxbay want to customize this

 .system <- function(...) {

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