Moved file import away from greedyMix() (#25)

R/greedyMix.R

@@ -13,40 +13,5 @@
 #' data <- system.file("extdata", "FASTA_clustering_haploid.fasta", package = "rBAPS")
 #' greedyMix(data)
 greedyMix <- function(data, format, verbose = TRUE) {
-  # Parsing data format ------------------------------------------------------
-
-  if (missing(format)) {
-    format <- gsub(".*\\.(.+)$", "\\1", data)
-    message("Format not provided. Guessing from file extension: ", format)
-  }
-  format <- tolower(format)
-
-  # Dispatching to proper loading function -----------------------------------
-
-  if (format == "fasta") {
-    out <- load_fasta(data)
-  } else if (format == "vcf") {
-    out <- vcfR::read.vcfR(data, verbose = verbose)
-  } else if (format == "sam") {
-    stop(
-      "SAM files not directly supported. ",
-      "Install the samtools software and execute\n\n",
-      "samtools view -b ", data, " > out_file.bam\n\nto convert to BAM ",
-      "and try running this function again with 'format=BAM'"
-    )
-  } else if (format == "bam") {
-    out <- Rsamtools::scanBam(data)
-  } else if (format == "genepop") {
-    if (toupper(adegenet::.readExt(data)) == "TXT") {
-      message("Creating a copy of the file with the .gen extension")
-      dataGen <- gsub("txt", "gen", data)
-      file.copy(data, dataGen)
-      out <- adegenet::read.genepop(dataGen)
-    } else {
-      out <- adegenet::read.genepop(data)
-    }
-  } else {
-    stop("Format not supported.")
-  }
-  return(out)
+  data <- importFile(data, format, verbose)
 }

R/importFile.R

@@ -0,0 +1,38 @@
+importFile <- function(data, format, verbose) {
+  # Parsing data format ------------------------------------------------------
+
+  if (missing(format)) {
+    format <- gsub(".*\\.(.+)$", "\\1", data)
+    message("Format not provided. Guessing from file extension: ", format)
+  }
+  format <- tolower(format)
+
+  # Dispatching to proper loading function -----------------------------------
+
+  if (format == "fasta") {
+    out <- load_fasta(data)
+  } else if (format == "vcf") {
+    out <- vcfR::read.vcfR(data, verbose = verbose)
+  } else if (format == "sam") {
+    stop(
+      "SAM files not directly supported. ",
+      "Install the samtools software and execute\n\n",
+      "samtools view -b ", data, " > out_file.bam\n\nto convert to BAM ",
+      "and try running this function again with 'format=BAM'"
+    )
+  } else if (format == "bam") {
+    out <- Rsamtools::scanBam(data)
+  } else if (format == "genepop") {
+    if (toupper(adegenet::.readExt(data)) == "TXT") {
+      message("Creating a copy of the file with the .gen extension")
+      dataGen <- gsub("txt", "gen", data)
+      file.copy(data, dataGen)
+      out <- adegenet::read.genepop(dataGen)
+    } else {
+      out <- adegenet::read.genepop(data)
+    }
+  } else {
+    stop("Format not supported.")
+  }
+  return(out)
+}