diff --git a/CHANGELOG.md b/CHANGELOG.md index 50c14ff..3875d58 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,7 +1,7 @@ CHANGELOG --------- -#### Version 1.0.11 (2024.03.27) +#### Version 1.0.11 (2024.04.08) * Minor fixes to tabular statistics file creation * A coverage of 0 for a window is always labeled as low coverage diff --git a/DESCRIPTION b/DESCRIPTION index d37d561..757f2f0 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: PACVr Version: 1.0.11 -Date: 2024-03-27 +Date: 2024-04-08 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 e66763c..8d2b47b 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="2024.03.27.0311" +#version="2024.04.08.0223" AnalysisSpecs <- R6Class("AnalysisSpecs", public = list( diff --git a/R/GBKData.R b/R/GBKData.R index c349bbc..163a225 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="2024.03.27.0311" +#version="2024.04.08.0223" GBKData <- R6Class("GBKData", public = list( diff --git a/R/IROps.R b/R/IROps.R index 2ce1ca5..a1e1b3f 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="2024.03.27.0311" +#version="2024.04.08.0223" checkIREquality <- function(gbkData, analysisSpecs) { diff --git a/R/OutputSpecs.R b/R/OutputSpecs.R index 82376bf..3ac999c 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="2024.03.27.0311" +#version="2024.04.08.0223" OutputSpecs <- R6Class("OutputSpecs", public = list( diff --git a/R/PACVr.R b/R/PACVr.R index 3def46b..7b7767b 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="2024.03.27.0311" +#version="2024.04.08.0223" PACVr.read.gb <- function(gbkFile) { gbkRaw <- getGbkRaw(gbkFile) diff --git a/R/RCircosOps.R b/R/RCircosOps.R index 7cb55da..d6539e5 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="2024.03.27.0311" +#version="2024.04.08.0223" # 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 55e23ab..172bd7d 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="2024.03.27.0311" +#version="2024.04.08.0223" PACVr.compileCovStats <- function(gbkData, coverageRaw, diff --git a/R/coverageCalcOps.R b/R/coverageCalcOps.R index 6bb04f7..b6d5827 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="2024.03.27.0311" +#version="2024.04.08.0223" CovCalc <- function(coverageRaw, windowSize = 250, diff --git a/R/customRead.gb.R b/R/customRead.gb.R index 3822d84..e165aa7 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="2024.03.27.0311" +#version="2024.04.08.0223" read.gbWithHandling <- function(gbkRaw, count=0) { gbkData <- tryCatch({ diff --git a/R/helpers.R b/R/helpers.R index 8a5ea3f..906f32d 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="2024.03.27.0311" +#version="2024.04.08.0223" 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 14cacfc..5359a25 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="2024.03.27.0311" +#version="2024.04.08.0223" PACVr.parseGenes <- function (gbkSeqFeatures) { # Function to extract gene information from Genbank flatfile data diff --git a/R/quadripOps.R b/R/quadripOps.R index 057334a..0e48512 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="2024.03.27.0311" +#version="2024.04.08.0223" FilterByKeywords <- function(allRegions, where) { # Function to filter list based on genomic keywords diff --git a/R/readingOps.R b/R/readingOps.R index f9ab072..df3a236 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="2024.03.27.0311" +#version="2024.04.08.0223" read.gbSeqFeaturesAdapt <- function(gbkData, analysisSpecs) { gbkSeqFeatures <- read.gbSeqFeatures(gbkData, diff --git a/R/visualisationOps.R b/R/visualisationOps.R index 6c2a676..b6802a9 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="2024.03.27.0311" +#version="2024.04.08.0223" vizWithRCircos <- function(gbkData, coverage, diff --git a/R/writingOps.R b/R/writingOps.R index 72ac64d..c924905 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="2024.03.27.0311" +#version="2024.04.08.0223" writeCovTables <- function(covData, sample_name, dir) { writeStatsTable(covData$ir_genes, sample_name, dir, "coverage.genes")