Update documentation for version

michaelgruenstaeudl · May 25, 2024 · db3e731 · db3e731
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,7 +1,7 @@
 CHANGELOG
 ---------
 
-#### Version 1.1.2 (2024.05.24)
+#### Version 1.1.2 (2024.05.25)
 * Updates to summary tabular statistics files
   * Inclusion of unpartitioned statistics for coding and noncoding regions summaries
   * Standardize name of summary groups to `Chromosome`

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: PACVr
 Version: 1.1.2
-Date: 2024-05-24
+Date: 2024-05-25
 Title: Plastome Assembly Coverage Visualization
 Authors@R: c(person("Gregory", "Smith", role=c("ctb")),
              person("Nils", "Jenke", role=c("ctb")),

diff --git a/R/AnalysisSpecs.R b/R/AnalysisSpecs.R
@@ -1,7 +1,7 @@
 #!/usr/bin/env RScript
 #contributors=c("Gregory Smith", "Nils Jenke", "Michael Gruenstaeudl")
 #email="m_gruenstaeudl@fhsu.edu"
-#version="2024.05.24.2053"
+#version="2024.05.25.0158"
 
 AnalysisSpecs <- R6Class("AnalysisSpecs",
   public = list(

diff --git a/R/GBKData.R b/R/GBKData.R
@@ -1,7 +1,7 @@
 #!/usr/bin/env RScript
 #contributors=c("Gregory Smith", "Nils Jenke", "Michael Gruenstaeudl")
 #email="m_gruenstaeudl@fhsu.edu"
-#version="2024.05.24.2053"
+#version="2024.05.25.0158"
 
 GBKData <- R6Class("GBKData",
   public = list(

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="2024.05.24.2053"
+#version="2024.05.25.0158"
 
 checkIREquality <- function(gbkData,
                             analysisSpecs) {

diff --git a/R/OutputSpecs.R b/R/OutputSpecs.R
@@ -1,7 +1,7 @@
 #!/usr/bin/env RScript
 #contributors=c("Gregory Smith", "Nils Jenke", "Michael Gruenstaeudl")
 #email="m_gruenstaeudl@fhsu.edu"
-#version="2024.05.24.2053"
+#version="2024.05.25.0158"
 
 OutputSpecs <- R6Class("OutputSpecs",
   public = list(

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="2024.05.24.2053"
+#version="2024.05.25.0158"
 
 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="2024.05.24.2053"
+#version="2024.05.25.0158"
 
 
 # The following R functions were taken from the R package RCircos and then modified.

diff --git a/R/compileStats.R b/R/compileStats.R
@@ -1,7 +1,7 @@
 #!/usr/bin/env RScript
 #contributors=c("Gregory Smith", "Nils Jenke", "Michael Gruenstaeudl")
 #email="m_gruenstaeudl@fhsu.edu"
-#version="2024.05.24.2053"
+#version="2024.05.25.0158"
 
 PACVr.compileCovStats <- function(gbkData,
                                   coverageRaw,

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="2024.05.24.2053"
+#version="2024.05.25.0158"
 
 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="2024.05.24.2053"
+#version="2024.05.25.0158"
 
 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="2024.05.24.2053"
+#version="2024.05.25.0158"
 
 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="2024.05.24.2053"
+#version="2024.05.25.0158"
 
 PACVr.parseGenes <- 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="2024.05.24.2053"
+#version="2024.05.25.0158"
 
 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="2024.05.24.2053"
+#version="2024.05.25.0158"
 
 read.gbSeqFeaturesAdapt <- function(gbkData, analysisSpecs) {
   gbkSeqFeatures <- read.gbSeqFeatures(gbkData,

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="2024.05.24.2053"
+#version="2024.05.25.0158"
 
 vizWithRCircos <- function(gbkData,
                                  coverage,

diff --git a/R/writingOps.R b/R/writingOps.R
@@ -1,7 +1,7 @@
 #!/usr/bin/env RScript
 #contributors=c("Gregory Smith", "Nils Jenke", "Michael Gruenstaeudl")
 #email="m_gruenstaeudl@fhsu.edu"
-#version="2024.05.24.2053"
+#version="2024.05.25.0158"
 
 writeCovTables <- function(covData, sample_name, dir) {
   writeStatsTable(covData$ir_genes, sample_name, dir, "coverage.genes")