Update documentation for version

michaelgruenstaeudl · Feb 28, 2024 · 3ccf9b0 · 3ccf9b0
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,6 +1,6 @@
 CHANGELOG
 ---------
-#### Version 1.0.9 (2024.02.29)
+#### Version 1.0.9 (2024.02.28)
 * Improving variable and file names
 
 #### Version 1.0.8 (2024.02.28)

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: PACVr
-Version: 1.0.8
+Version: 1.0.9
 Date: 2024-02-28
 Title: Plastome Assembly Coverage Visualization
 Authors@R: c(person("Gregory", "Smith", role=c("ctb")),

diff --git a/R/IROps.R b/R/IROps.R
@@ -1,7 +1,7 @@
 #!/usr/bin/env RScript
 #contributors=c("Gregory Smith", "Nils Jenke", "Michael Gruenstaeudl")
 #email="m_gruenstaeudl@fhsu.edu"
-#version="2024.02.28.0051"
+#version="2024.02.28.0231"
 
 checkIREquality <- function(gbkSeq, regions, dir, sample_name) {
   if ("IRb" %in% regions[, 4] && "IRa" %in% regions[, 4]) {

diff --git a/R/PACVr.R b/R/PACVr.R
@@ -1,7 +1,7 @@
 #!/usr/bin/env RScript
 #contributors=c("Gregory Smith", "Nils Jenke", "Michael Gruenstaeudl")
 #email="m_gruenstaeudl@fhsu.edu"
-#version="2024.02.28.0051"
+#version="2024.02.28.0231"
 
 PACVr.read.gb <- function(gbkFile) {
   gbkRaw <- getGbkRaw(gbkFile)

diff --git a/R/RCircosOps.R b/R/RCircosOps.R
@@ -1,7 +1,7 @@
 #!/usr/bin/env RScript
 #contributors=c("Gregory Smith", "Nils Jenke", "Michael Gruenstaeudl")
 #email="m_gruenstaeudl@fhsu.edu"
-#version="2024.02.28.0051"
+#version="2024.02.28.0231"
 
 
 # The following R functions were taken from the R package RCircos and then modified.

diff --git a/R/coverageCalcOps.R b/R/coverageCalcOps.R
@@ -1,7 +1,7 @@
 #!/usr/bin/env RScript
 #contributors=c("Gregory Smith", "Nils Jenke", "Michael Gruenstaeudl")
 #email="m_gruenstaeudl@fhsu.edu"
-#version="2024.02.28.0051"
+#version="2024.02.28.0231"
 
 CovCalc <- function(coverageRaw,
                     windowSize = 250,

diff --git a/R/customRead.gb.R b/R/customRead.gb.R
@@ -1,7 +1,7 @@
 #!/usr/bin/env RScript
 #contributors=c("Gregory Smith", "Nils Jenke", "Michael Gruenstaeudl")
 #email="m_gruenstaeudl@fhsu.edu"
-#version="2024.02.28.0051"
+#version="2024.02.28.0231"
 
 read.gbWithHandling <- function(gbkRaw, count=0) {
   gbkData <- tryCatch({

diff --git a/R/helpers.R b/R/helpers.R
@@ -1,7 +1,7 @@
 #!/usr/bin/env RScript
 #contributors=c("Gregory Smith", "Nils Jenke", "Michael Gruenstaeudl")
 #email="m_gruenstaeudl@fhsu.edu"
-#version="2024.02.28.0051"
+#version="2024.02.28.0231"
 
 HistCol <- function(cov, threshold, relative, logScale) {
   # Function to generate color vector for histogram data

diff --git a/R/parsingOps.R b/R/parsingOps.R
@@ -1,7 +1,7 @@
 #!/usr/bin/env RScript
 #contributors=c("Gregory Smith", "Nils Jenke", "Michael Gruenstaeudl")
 #email="m_gruenstaeudl@fhsu.edu"
-#version="2024.02.28.0051"
+#version="2024.02.28.0231"
 
 ExtractAllGenes <- function(gbkSeqFeatures) {
   # Function to extract gene information from Genbank flatfile data

diff --git a/R/quadripOps.R b/R/quadripOps.R
@@ -1,7 +1,7 @@
 #!/usr/bin/env RScript
 #contributors=c("Gregory Smith", "Nils Jenke", "Michael Gruenstaeudl")
 #email="m_gruenstaeudl@fhsu.edu"
-#version="2024.02.28.0051"
+#version="2024.02.28.0231"
 
 FilterByKeywords <- function(allRegions, where) {
   # Function to filter list based on genomic keywords

diff --git a/R/readingOps.R b/R/readingOps.R
@@ -1,7 +1,7 @@
 #!/usr/bin/env RScript
 #contributors=c("Gregory Smith", "Nils Jenke", "Michael Gruenstaeudl")
 #email="m_gruenstaeudl@fhsu.edu"
-#version="2024.02.28.0051"
+#version="2024.02.28.0231"
 
 read.gbSeqFeatures <- function(gbkData, analysisSpecs) {
   fileDF <- data.frame()

diff --git a/R/visualisationOps.R b/R/visualisationOps.R
@@ -1,7 +1,7 @@
 #!/usr/bin/env RScript
 #contributors=c("Gregory Smith", "Nils Jenke", "Michael Gruenstaeudl")
 #email="m_gruenstaeudl@fhsu.edu"
-#version="2024.02.28.0051"
+#version="2024.02.28.0231"
 
 vizWithRCircos <- function(gbkData,
                                  coverage,