From 8ce9f3af04cf6beae319663113c7d6724b5bb79a Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <w.l.netto@medisin.uio.no>
Date: Mon, 23 Jan 2023 11:21:16 +0100
Subject: [PATCH 1/3] Translated testFastaData() (#3)

---
 R/testFastaData.R | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 R/testFastaData.R

diff --git a/R/testFastaData.R b/R/testFastaData.R
new file mode 100644
index 0000000..ad88256
--- /dev/null
+++ b/R/testFastaData.R
@@ -0,0 +1,19 @@
+testFastaData <- function(inFile) {
+  #  added by Lu Cheng, 11.11.2012
+  if (!exists(inFile, 'file')) {
+    stop('Fasta file ', inFile, ' does not exist!')
+  }
+
+  seqs <- load_fasta(inFile)
+  heds <- colnames(seqs)
+  ninds <- length(seqs)
+
+  data <- as.matrix(seqs)
+  newData <- ones(size(data)) * -9
+  newData[toupper(data) == 'A'] <- 1
+  newData[toupper(data) == 'C'] <- 2
+  newData[toupper(data) == 'G'] <- 3
+  newData[toupper(data) == 'T'] <- 4
+  data <- c(newData, t(1:ninds))
+  return(list("ninds" = ninds, "data" = data, "heds" = heds))
+}

From 257046dc5f101789c38ccfdadfe928ccd9f15d28 Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <w.l.netto@medisin.uio.no>
Date: Mon, 23 Jan 2023 11:22:01 +0100
Subject: [PATCH 2/3] Fixed synxtax of zeallot call (#3)

---
 R/dec2bitv.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/dec2bitv.R b/R/dec2bitv.R
index db680a8..abe5169 100644
--- a/R/dec2bitv.R
+++ b/R/dec2bitv.R
@@ -10,7 +10,7 @@ dec2bitv <- function(d, n) {
   d <- d[]
 
   f <- e <- NA
-  c(f, e) <- matlab2r::log2(max(d)) # How many digits do we need to represent the numbers?
-    bits <- floor(d * 2 ^ (seq(1 - max(n, e), 0))) %% 2
+  c(f, e) %<-% matlab2r::log2(max(d)) # How many digits do we need to represent the numbers?
+  bits <- floor(d * 2 ^ (seq(1 - max(n, e), 0))) %% 2
   return(bits)
 }

From 0f470725990f12259d689eef217134c8b5d870af Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <w.l.netto@medisin.uio.no>
Date: Mon, 23 Jan 2023 11:22:06 +0100
Subject: [PATCH 3/3] Increment version number to 0.0.0.9016

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 47170d2..2810550 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: rBAPS
 Title: Bayesian Analysis of Population Structure
-Version: 0.0.0.9015
+Version: 0.0.0.9016
 Date: 2020-11-09
 Authors@R:
     c(