Implemented an improved version to check whether bams have been mappe…

…d to same reference genome
PeeperLab · Jun 10, 2015 · bebaee5 · bebaee5
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Showing 2 changed files with 16 additions and 14 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,12 +1,12 @@
 Package: CopywriteR
 Type: Package
 Title: Copy number information from targeted sequencing using off-target reads
-Version: 2.0.4
+Version: 2.0.5
 Date: 2014-09-23
 Author: Thomas Kuilman
 Maintainer: Thomas Kuilman <t.kuilman@nki.nl>
 Imports: matrixStats, gtools, data.table, S4Vectors, chipseq, IRanges, Rsamtools, DNAcopy, GenomicAlignments, GenomicRanges, CopyhelpeR, GenomeInfoDb, futile.logger
-Depends: R(>= 3.2), BiocParallel
+Depends: R(>= 3.1), 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 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.

diff --git a/R/CopywriteR.R b/R/CopywriteR.R
@@ -137,10 +137,10 @@ CopywriteR <- function(sample.control, destination.folder, reference.folder,
             header <- scanBamHeader(samp)
             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)
-            prefixes <- append(prefixes, gsub("[[:digit:]]|X|Y|M|T",
-                                              "", chr.names[1])[1])
+    				chr.names <- c(chr.names, list(current.chr.names))
+		    		chr.lengths <- c(chr.lengths, list(header[[1]]$targets))
+    				prefixes <- append(prefixes, gsub("[[:digit:]]|X|Y|M|T",
+		    																			"", current.chr.names)[1])
         }
     }, error = function(e) {
         stop(.wrap("The BAM file header of file", sQuote(samp), "is corrupted",
@@ -162,14 +162,16 @@ CopywriteR <- function(sample.control, destination.folder, reference.folder,
         stop(.wrap("The bam files have different chromosome name prefixes.",
                    "Please adjust the .bam files such that they contain the",
                    "same chromosome notation."))
-    } else if (!length(unique(chr.names)) * length(sample.paths) == length(chr.names)) {
-        stop(.wrap("The bam files have been mapped to different reference",
-                   "genomes. Please run only .bam files mapped to the same",
-                   "reference genome together."))
-    } else if (!length(unique(chr.lengths)) * length(sample.paths) == length(chr.lengths)) {
-        stop(.wrap("The bam files have different chromosome names. Please",
-                   "adjust the .bam files such that they contain the same",
-                   "chromosome notation."))
+		} else if (length(chr.names) > 1) {
+		    if (!Reduce(function(x,y) {identical(x,y)}, chr.names)) {
+						stop(.wrap("The bam files have been mapped to different reference",
+											 "genomes (the chromosome names are not identical). Please run",
+											 "only .bam files mapped to the same reference genome together."))
+				} else if (!Reduce(function(x,y) {identical(x,y)}, chr.lengths)) {
+						stop(.wrap("The bam files have been mapped to different reference",
+											 "genomes (the chromosome lengths are not identical). Please run",
+											 "only .bam files mapped to the same reference genome together."))
+		    }
     } else {
         prefixes <- prefixes[1]