Added SAM/BAM support (closes #18)

R/greedyMix.R

@@ -1,9 +1,11 @@
 #' @title Clustering of individuals
 #' @param data data file
-#' @param format Format of the data c("FASTA", "VCF" ,"SAM", or "GenePop")
+#' @param format Format of the data c("FASTA", "VCF" ,"BAM", or "GenePop")
 #' @param verbose if \code{TRUE}, prints extra output information
 #' @importFrom utils read.delim
 #' @importFrom vcfR read.vcfR
+#' @references Samtools: a suite of programs for interacting
+#' with high-throughput sequencing data. <http://www.htslib.org/>
 #' @export
 greedyMix <- function(data, format, verbose = TRUE) {
 	format <- tolower(format)
@@ -12,8 +14,14 @@ greedyMix <- function(data, format, verbose = TRUE) {
 	} else if (format == "vcf") {
 		out <- vcfR::read.vcfR(data, verbose = verbose)
 	} else if (format == "sam") {
-		stop("SAM files not yet supported." )
-		# TODO #18: implement load_sam()
+		stop(
+			"SAM files not directly supported. ",
+			"Install the samtools software and execute ",
+			"'samtools view -b in_file.sam > out_file.bam' to convert to BAM ",
+			"and try running this function again with 'format=BAM'"
+		)
+	} else if (format == "bam") {
+		out <- Rsamtools::scanBam(data)
 	} else if (format == "genepop") {
 		# TODO #19: implement load_genepop()
 		stop("GenePop files not yet supported." )