From a296f9f8fbc73d8466209ab62e84db0a6e86a3b2 Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <w.l.netto@medisin.uio.no>
Date: Fri, 3 Sep 2021 08:43:37 +0200
Subject: [PATCH] greedyMix changed to channel data load (close #16)

---
 R/greedyMix.R    | 37 ++++++++++++++++++++-----------------
 man/greedyMix.Rd | 15 +++------------
 2 files changed, 23 insertions(+), 29 deletions(-)

diff --git a/R/greedyMix.R b/R/greedyMix.R
index 83472e4..8b79573 100644
--- a/R/greedyMix.R
+++ b/R/greedyMix.R
@@ -1,20 +1,23 @@
 #' @title Clustering of individuals
-#' @param tietue File
-#' @param format Format of the data ("BAPS", "GenePop" or "Preprocessed")
-#' @param savePreProcessed Save the pre-processed data?
-#' @param filePreProcessed Is the file already processed?
+#' @param data data file
+#' @param format Format of the data c("FASTA", "VCF" ,"SAM", or "GenePop")
 #' @importFrom utils read.delim
 #' @export
-greedyMix <- function(
-	tietue,
-	format           = NULL,
-	savePreProcessed = NULL,
-	filePreProcessed = NULL
-) {
-	stop(
-		"greedyMix() has been superseded by load_fasta().",
-		" Please change your code to use the latter instead of the former.",
-		" If you believe the error is internal to rBAPS, please open",
-		" a new issue (link on the package DESCRIPTION file)."
-		)
-}
+greedyMix <- function(data, format) {
+	format <- tolower(format)
+	if (format == "fasta") {
+		out <- load_fasta(data)
+	} else if (format == "vcf") {
+		stop("VCF files not yet supported." )
+		# TODO #16: implement load_vcf()
+	} else if (format == "sam") {
+		stop("SAM files not yet supported." )
+		# TODO #16: implement load_sam()
+	} else if(format == "genepop") {
+		# TODO #16: implement load_genepop()
+		stop("GenePop files not yet supported." )
+	} else {
+		stop("Format not supported.")
+	}
+	return(out)
+}
\ No newline at end of file
diff --git a/man/greedyMix.Rd b/man/greedyMix.Rd
index b8a04cb..7117437 100644
--- a/man/greedyMix.Rd
+++ b/man/greedyMix.Rd
@@ -4,21 +4,12 @@
 \alias{greedyMix}
 \title{Clustering of individuals}
 \usage{
-greedyMix(
-  tietue,
-  format = NULL,
-  savePreProcessed = NULL,
-  filePreProcessed = NULL
-)
+greedyMix(data, format)
 }
 \arguments{
-\item{tietue}{File}
+\item{data}{data file}
 
-\item{format}{Format of the data ("BAPS", "GenePop" or "Preprocessed")}
-
-\item{savePreProcessed}{Save the pre-processed data?}
-
-\item{filePreProcessed}{Is the file already processed?}
+\item{format}{Format of the data c("FASTA", "VCF" ,"SAM", or "GenePop")}
 }
 \description{
 Clustering of individuals