Merge remote-tracking branch 'upstream/devel' into devel

Author: lima1

DESCRIPTION

@@ -2,8 +2,8 @@ Package: PureCN
 Type: Package
 Title: Copy number calling and SNV classification using
     targeted short read sequencing
-Version: 2.15.3
-Date: 2025-04-23
+Version: 2.15.4
+Date: 2025-07-22
 Authors@R: c(person("Markus", "Riester",
                     role = c("aut", "cre"),
                     email = "markus.riester@novartis.com",
@@ -30,6 +30,7 @@ Imports:
     stats,
     utils,
     SummarizedExperiment,
+    Seqinfo,
     GenomeInfoDb,
     GenomicFeatures,
     Rsamtools,

NAMESPACE

@@ -53,17 +53,9 @@ importFrom(BiocGenerics,unstrand)
 importFrom(Biostrings,DNAStringSet)
 importFrom(Biostrings,DNAStringSetList)
 importFrom(Biostrings,letterFrequency)
-importFrom(GenomeInfoDb,"genome<-")
-importFrom(GenomeInfoDb,"seqlengths<-")
-importFrom(GenomeInfoDb,"seqlevels<-")
 importFrom(GenomeInfoDb,"seqlevelsStyle<-")
 importFrom(GenomeInfoDb,genomeStyles)
-importFrom(GenomeInfoDb,rankSeqlevels)
-importFrom(GenomeInfoDb,seqlengths)
-importFrom(GenomeInfoDb,seqlevelsInUse)
 importFrom(GenomeInfoDb,seqlevelsStyle)
-importFrom(GenomeInfoDb,seqnames)
-importFrom(GenomeInfoDb,sortSeqlevels)
 importFrom(GenomicFeatures,cdsByOverlaps)
 importFrom(GenomicFeatures,exonsByOverlaps)
 importFrom(GenomicFeatures,transcriptsByOverlaps)
@@ -86,6 +78,14 @@ importFrom(S4Vectors,expand)
 importFrom(S4Vectors,mcols)
 importFrom(S4Vectors,queryHits)
 importFrom(S4Vectors,subjectHits)
+importFrom(Seqinfo,"genome<-")
+importFrom(Seqinfo,"seqlengths<-")
+importFrom(Seqinfo,"seqlevels<-")
+importFrom(Seqinfo,rankSeqlevels)
+importFrom(Seqinfo,seqlengths)
+importFrom(Seqinfo,seqlevelsInUse)
+importFrom(Seqinfo,seqnames)
+importFrom(Seqinfo,sortSeqlevels)
 importFrom(SummarizedExperiment,rowRanges)
 importFrom(VGAM,Coef)
 importFrom(VGAM,betabinomial)

R/calculateMappingBiasVcf.R

@@ -133,7 +133,7 @@ calculateMappingBiasVcf <- function(normal.panel.vcf.file,
 #'
 #' @export calculateMappingBiasGatk4
 #' @importFrom data.table dcast
-#' @importFrom GenomeInfoDb rankSeqlevels
+#' @importFrom Seqinfo rankSeqlevels
 calculateMappingBiasGatk4 <- function(workspace, reference.genome,
                                     min.normals = 1,
                                     min.normals.betafit = 7,

R/filterVcf.R

@@ -64,8 +64,8 @@
 #' vcf.filtered <- filterVcfBasic(vcf)
 #'
 #' @export filterVcfBasic
-#' @importFrom GenomeInfoDb seqnames seqlevelsStyle seqlevelsStyle<-
-#'             genomeStyles sortSeqlevels
+#' @importFrom Seqinfo seqnames sortSeqlevels
+#' @importFrom GenomeInfoDb seqlevelsStyle seqlevelsStyle<- genomeStyles
 #' @importFrom SummarizedExperiment rowRanges
 #' @importFrom stats pbeta
 filterVcfBasic <- function(vcf, tumor.id.in.vcf = NULL,

R/preprocessIntervals.R

@@ -62,7 +62,7 @@
 #' @export preprocessIntervals
 #' @importFrom BiocGenerics unstrand score
 #' @importFrom Biostrings letterFrequency
-#' @importFrom GenomeInfoDb seqlengths seqlevelsInUse seqlevels<- seqlengths<-
+#' @importFrom Seqinfo seqlengths seqlevelsInUse seqlevels<- seqlengths<-
 #' @importFrom GenomicRanges tileGenome
 #' @importFrom S4Vectors mcols
 #' @importFrom rtracklayer import

R/setMappingBiasVcf.R

@@ -36,7 +36,7 @@
 #' vcf.bias <- setMappingBiasVcf(vcf)        
 #' 
 #' @export setMappingBiasVcf
-#' @importFrom GenomeInfoDb genome<-
+#' @importFrom Seqinfo genome<-
 setMappingBiasVcf <- function(vcf, tumor.id.in.vcf = NULL, mapping.bias.file = NULL,
 smooth = TRUE, smooth.n = 5) {
     if (is.null(tumor.id.in.vcf)) {

tests/testthat/test_getSexFromCoverage.R

@@ -1,5 +1,7 @@
 context("getSexFromCoverage")
 
+library(GenomeInfoDb)  # for renameSeqlevels()
+
 tumor.coverage.file <- system.file("extdata", "example_tumor.txt.gz", 
     package = "PureCN")
 coverage <- readCoverageFile(tumor.coverage.file)