@@ -2,8 +2,8 @@ Package: PureCN

 Type: Package

 Title: Copy number calling and SNV classification using

     targeted short read sequencing

-Version: 1.23.10

-Date: 2021-08-07

+Version: 1.23.11

+Date: 2021-08-10

 Authors@R: c(person("Markus", "Riester",

                     role = c("aut", "cre"),

                     email = "[email protected]",

@@ -33,6 +33,7 @@ Imports:

     GenomeInfoDb,

     GenomicFeatures,

     Rsamtools,

+    Biobase,

     Biostrings,

     BiocGenerics,

     rtracklayer,

@@ -44,6 +44,7 @@ export(setPriorVcf)

 import(DNAcopy)

 import(IRanges)

 import(VariantAnnotation)

+importFrom(Biobase,package.version)

 importFrom(BiocGenerics,score)

 importFrom(BiocGenerics,unstrand)

 importFrom(Biostrings,DNAStringSet)

@@ -9,6 +9,7 @@ SIGNIFICANT USER-VISIBLE CHANGES

       off-target regions in high quality samples where those minor off-sets

       sometimes exceeded the noise.

     o Added min.variants argument to runAbsoluteCN

+    o Added PureCN version to runAbsoluteCN results object (ret$version)

 BUGFIXES

@@ -265,6 +265,7 @@

 #' @import DNAcopy

 #' @import IRanges

 #' @import VariantAnnotation

+#' @importFrom Biobase package.version

 #' @importFrom GenomicRanges GRanges tile

 #' @importFrom stats complete.cases dbeta dnorm dunif runif weighted.mean

 #'             dbinom C

@@ -914,7 +915,7 @@ runAbsoluteCN <- function(normal.coverage.file = NULL,

         p <- sol$purity

         if (!is.null(vcf.file)) {

             flog.info("Fitting variants with %s model for local optimum %i/%i...",

-                model, sol$candidate.id, nrow(candidate.solutions$candidates), p)

+                model, sol$candidate.id, nrow(candidate.solutions$candidates))

         }

         if (sol$fraction.subclonal > max.non.clonal) {

             .stopRuntimeError(".fitSolution received high subclonal solution.")

@@ -1124,6 +1125,7 @@ runAbsoluteCN <- function(normal.coverage.file = NULL,

             args = list(

                 filterVcf = args.filterVcf[vapply(args.filterVcf, object.size, double(1)) < 1000],

                 filterIntervals = args.filterIntervals[vapply(args.filterIntervals, object.size, double(1)) < 1000])

-        )

+        ),

+        version = package.version("PureCN")

     )

 }

@@ -27,7 +27,8 @@ test_that("VCF is not necessary to produce output", {

         test.purity = seq(0.4, 0.7, by = 0.05), min.ploidy = 1.5,

         max.ploidy = 2.4, max.candidate.solutions = 1,

         BPPARAM = BiocParallel::bpparam())

-

+    

+    expect_true(!is.null(ret$version))

     tmpFile <- tempfile(fileext = ".rds")

     saveRDS(ret, tmpFile)

     createCurationFile(tmpFile)

@@ -151,6 +152,7 @@ test_that("Example data with VCF produces expected output", {

         max.candidate.solutions = 1, min.ploidy = 1.5, max.ploidy = 2.1,

         vcf.field.prefix = "PureCN."

     )

+    expect_true(!is.null(ret$version))

     expect_equal(ret$results[[1]]$fraction.balanced, 0.2, tolerance = 0.02)

     s <- predictSomatic(ret)

     expect_equal(s$AR / s$MAPPING.BIAS, s$AR.ADJUSTED)