From 3ccf9b00d34d99e4458a6c43457d46781e420c8d Mon Sep 17 00:00:00 2001 From: michaelgruenstaeudl Date: Wed, 28 Feb 2024 02:31:27 +0000 Subject: [PATCH] Update documentation for version --- CHANGELOG.md | 2 +- DESCRIPTION | 2 +- R/IROps.R | 2 +- R/PACVr.R | 2 +- R/RCircosOps.R | 2 +- R/coverageCalcOps.R | 2 +- R/customRead.gb.R | 2 +- R/helpers.R | 2 +- R/parsingOps.R | 2 +- R/quadripOps.R | 2 +- R/readingOps.R | 2 +- R/visualisationOps.R | 2 +- 12 files changed, 12 insertions(+), 12 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7b8db74..36dd4d9 100644 --- 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 index d0e7753..a59cd00 100644 --- 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 index ce5070e..d6f997d 100644 --- 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 index e45a27f..793b1e6 100644 --- 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 index 03f6dd5..0132f1e 100644 --- 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 index a454ffc..9158644 100644 --- 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 index e6a2a78..7530078 100644 --- 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 index 7cb1405..3896b67 100644 --- 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 index 97d9f89..bd7eb17 100644 --- 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 index c7f3cd0..11311a0 100644 --- 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 index 63b6c75..b8f48d3 100644 --- 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 index 49d66a3..a7c106b 100644 --- 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,