Updated DESCRIPTION

DESCRIPTION

@@ -9,6 +9,6 @@ Imports: matrixStats, gtools, data.table, S4Vectors, chipseq, IRanges, Rsamtools
 Depends: R(>= 3.2), BiocParallel
 Suggests: BiocStyle, SCLCBam, snow
 URL: https://github.com/PeeperLab/CopywriteR
-Description: CopywriteR extracts DNA copy number information from targeted sequencing by utiizing off-target sequence reads. It allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. Thereby, CopywriteR constitutes a widely applicable alternative to available tools.
+Description: CopywriteR extracts DNA copy number information from targeted sequencing by utiizing off-target reads. It allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. Thereby, CopywriteR constitutes a widely applicable alternative to available copy number detection tools.
 License: GPL-2
 biocViews: TargetedResequencing, ExomeSeq, CopyNumberVariation, Preprocessing, Visualization, Coverage

R/CopywriteR.R

@@ -135,7 +135,7 @@ CopywriteR <- function(sample.control, destination.folder, reference.folder,
     tryCatch({
         for (samp in sample.paths) {
             header <- scanBamHeader(samp)
-            chr.sort.mode <- c(chr.sort.mode, header[[1]]$text$'@HD'[2])
+            chr.sort.mode <- c(chr.sort.mode, list(header[[1]]$text$'@HD'))
             current.chr.names <- names(header[[1]]$targets)
             chr.names <- c(chr.names, current.chr.names)
             chr.lengths <- c(chr.lengths, header[[1]]$targets)
@@ -149,11 +149,14 @@ CopywriteR <- function(sample.control, destination.folder, reference.folder,
                    "the script..."))
     })
 
-    if (!all(chr.sort.mode == "SO:coordinate")) {
+    chr.sort.mode <- unlist(lapply(chr.sort.mode, function(x) {
+        length(grep("SO:coordinate", x))
+    }))
+    if (any(chr.sort.mode == 0)) {
         stop(.wrap("The following .bam files are unsorted:"), "\n",
-             paste(sample.paths[which(!chr.sort.mode == "SO:coordinate")], "\n",
-             "Please sort these .bam files based on coordinates",
-             collapse = "\n"))
+             paste(sample.paths[which(chr.sort.mode == 0)],
+             collapse = "\n"), "\n",
+             "Please sort these .bam files based on coordinates")
     }
     if (!all(prefixes == prefixes[1])) {
         stop(.wrap("The bam files have different chromosome name prefixes.",