diff --git a/CHANGELOG.md b/CHANGELOG.md index 1bbf971..341eb1f 100644 --- 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 index 753481f..5c4ec4a 100644 --- 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 index 64b3321..24116b8 100644 --- 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 index 7039e39..3e882b4 100644 --- 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 index 8b55110..96f684b 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="2024.05.24.2053" +#version="2024.05.25.0158" checkIREquality <- function(gbkData, analysisSpecs) { diff --git a/R/OutputSpecs.R b/R/OutputSpecs.R index 7925fe7..0703dcb 100644 --- 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 index 096e27d..ba38fd4 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="2024.05.24.2053" +#version="2024.05.25.0158" PACVr.read.gb <- function(gbkFile) { gbkRaw <- getGbkRaw(gbkFile) diff --git a/R/RCircosOps.R b/R/RCircosOps.R index 4757c29..e6921d8 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="2024.05.24.2053" +#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 index 7a2904a..0ec3cf0 100644 --- 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 index 795aa30..e5cda3b 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="2024.05.24.2053" +#version="2024.05.25.0158" CovCalc <- function(coverageRaw, windowSize = 250, diff --git a/R/customRead.gb.R b/R/customRead.gb.R index 440e590..3cadd4e 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="2024.05.24.2053" +#version="2024.05.25.0158" read.gbWithHandling <- function(gbkRaw, count=0) { gbkData <- tryCatch({ diff --git a/R/helpers.R b/R/helpers.R index d8f4f5c..3d5c8a6 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="2024.05.24.2053" +#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 index d5330ce..496a9a4 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="2024.05.24.2053" +#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 index 6309f24..9589731 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="2024.05.24.2053" +#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 index 06c4158..4081747 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="2024.05.24.2053" +#version="2024.05.25.0158" read.gbSeqFeaturesAdapt <- function(gbkData, analysisSpecs) { gbkSeqFeatures <- read.gbSeqFeatures(gbkData, diff --git a/R/visualisationOps.R b/R/visualisationOps.R index caf14be..4f4f64d 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="2024.05.24.2053" +#version="2024.05.25.0158" vizWithRCircos <- function(gbkData, coverage, diff --git a/R/writingOps.R b/R/writingOps.R index a25d1e8..78b3b11 100644 --- 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")