Do not error out readCurationFile when CSV is missing and directory i…

…s not writable when re-generating it (closes lima1#196).

DESCRIPTION

@@ -2,8 +2,8 @@ Package: PureCN
 Type: Package
 Title: Copy number calling and SNV classification using
     targeted short read sequencing
-Version: 1.23.16
-Date: 2021-08-17
+Version: 1.23.17
+Date: 2021-08-20
 Authors@R: c(person("Markus", "Riester",
                     role = c("aut", "cre"),
                     email = "[email protected]",

NEWS

@@ -23,6 +23,8 @@ SIGNIFICANT USER-VISIBLE CHANGES
       - min.logr.sdev is now accessible in PureCN.R via --minlogrsdev
     o Added pairwise sample distances to normalDB output object helpful for
       finding noisy samples or batches in normal databases  
+    o Do not error out readCurationFile when CSV is missing and directory
+      is not writable when re-generating it (#196)
 
 BUGFIXES
 

R/filterIntervals.R

@@ -82,18 +82,19 @@ filterIntervals <- function(normal, tumor, log.ratio, seg.file,
         min.targeted.base, min.coverage)
 
     if (!is.null(normalDB)) {
-        min.coverage <- min.coverage / 10000
+        min.coverage <- 0
+        normal$average.coverage[is.na(normal$average.coverage)] <- min.coverage
         flog.info("normalDB provided. Setting minimum coverage for segmentation to %.4fX.", min.coverage)
     } else {
         flog.warn("No normalDB provided. Provide one for better results.")
     }
-
-    intervalsUsed <- .filterIntervalsCoverage(intervalsUsed, normal, tumor,
-        min.coverage)
 
     intervalsUsed <- .filterIntervalsTotalCounts(intervalsUsed, normal, tumor,
         min.total.counts)
 
+    intervalsUsed <- .filterIntervalsCoverage(intervalsUsed, normal, tumor,
+        min.coverage)
+
     intervalsUsed <- .filterIntervalsMappability(intervalsUsed, tumor,
         min.mappability)
 
@@ -224,6 +225,7 @@ normalDB.min.coverage, normalDB.max.missing) {
     }
     intervalsUsed
 }
+
 .filterIntervalsTotalCounts <- function(intervalsUsed, normal, tumor, min.total.counts) {
 
     well.covered.interval.idx <- (normal$counts + tumor$counts) >= min.total.counts
@@ -258,7 +260,7 @@ normalDB.min.coverage, normalDB.max.missing) {
 .filterIntervalsMappability <- function(intervalsUsed, tumor, min.mappability) {
     if (is.null(tumor$mappability) || all(is.na(tumor$mappability))) {
         return(intervalsUsed)
-    }    
+    }
     if (any(is.na(tumor$mappability))) {
         flog.warn("Some intervals do not have a mappability score, assuming they are fine.")
     }

R/readCurationFile.R

@@ -1,9 +1,9 @@
 #' Read curation file
-#' 
+#'
 #' Function that can be used to read the curated output of the
 #' \code{\link{runAbsoluteCN}} function.
-#' 
-#' 
+#'
+#'
 #' @param file.rds Output of the \code{\link{runAbsoluteCN}} function,
 #' serialized with \code{saveRDS}.
 #' @param file.curation Filename of a curation file that points to the correct
@@ -21,25 +21,29 @@
 #' @author Markus Riester
 #' @seealso \code{\link{runAbsoluteCN} \link{createCurationFile}}
 #' @examples
-#' 
+#'
 #' data(purecn.example.output)
 #' file.rds <- "Sample1_PureCN.rds"
-#' createCurationFile(file.rds) 
-#' # User can change the maximum likelihood solution manually in the generated 
+#' createCurationFile(file.rds)
+#' # User can change the maximum likelihood solution manually in the generated
 #' # CSV file. The correct solution is then loaded with readCurationFile.
-#' purecn.curated.example.output <-readCurationFile(file.rds) 
-#' 
+#' purecn.curated.example.output <-readCurationFile(file.rds)
+#'
 #' @export readCurationFile
 #' @importFrom utils read.csv
 readCurationFile <- function(file.rds,
 file.curation = gsub(".rds$", ".csv", file.rds),
-remove.failed = FALSE, report.best.only=FALSE, min.ploidy = NULL,
+remove.failed = FALSE, report.best.only = FALSE, min.ploidy = NULL,
 max.ploidy = NULL) {
     flog.info("Reading %s...", file.rds)
     res <- readRDS(file.rds)
     if (!file.exists(file.curation)) {
         flog.warn("Curation file %s does not exist, creating one.", file.curation)
-        createCurationFile(file.rds)
+        output <- try(createCurationFile(file.rds))
+        if (is(output, "try-error")) {
+            flog.warn("Failed to write %s: %s", file.curation, output)
+            return(res)
+        }
     }
     curation <- read.csv(file.curation, as.is=TRUE, nrows=1)
     .checkLogical <- function(field) {