From 3e4044bcec79f03c05a857c78631691b8d1e446f Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <w.l.netto@medisin.uio.no>
Date: Mon, 11 Sep 2023 12:37:25 +0200
Subject: [PATCH] Improved handling of supported formats for greedyMix() (#25)

---
 R/handleData.R | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/R/handleData.R b/R/handleData.R
index 97a8d32..6b4a209 100644
--- a/R/handleData.R
+++ b/R/handleData.R
@@ -21,13 +21,15 @@ handleData <- function(raw_data, format = "Genepop") {
   # koodi pienimm?ksi koodiksi, joka isompi kuin mik??n k?yt?ss?oleva koodi.
   # T?m?n j?lkeen funktio muuttaa alleelikoodit siten, ett?yhden lokuksen j
   # koodit saavat arvoja v?lill?1,...,noalle(j).
+  nloci <- switch(
+    tolower(format),
+    "genepop" = ncol(raw_data) - 1L,
+    "baps"    = ncol(raw_data) - 1L,
+    "fasta"   = ncol(raw_data),
+    "vcf"     = stop("VCF format not supported for processing yet"),
+    "bam"     = stop("BAM format not supported for processing yet")
+  )
   data <- as.matrix(raw_data)
-  if (format %in% c("genepop", "baps")) {
-    nloci <- size(raw_data, 2) - 1
-  } else {
-    nloci <- size(raw_data, 2)
-  }
-
   dataApu <- data[, 1:nloci]
   nollat <- matlab2r::find(dataApu == 0)
   if (!isempty(nollat)) {