Fix issue 63: filename length bug (#64)

* fix issue 63: Filename length restriction in R diffchrom script

README.md

@@ -16,7 +16,14 @@ The original script with a documentation of the underlying ideas can be found [h
 
 ## Change Logs
 
-* 1.2.73-2 (branch-specific change)
+* 1.2.73-202 (branch-specific change)
+  - PATCH: call of grDevices.pdf() in chrom_diff.r lead to unexpected 
+    (truncated to at most 511 characters) file name of output pdf 
+
+* 1.2.73-201 (branch-specific change)
+  - PATCH: explicit MBUFFER version can be specified for tbi-lsf environment
+
+* 1.2.73-2, 1.2.73-200 (branch-specific change)
   - Updated unidirectional WGBS read-reordering script from [here](https://github.com/cimbusch/TWGBS.git)
   - Actually include the WGBS read-reordering script
   - Improved error checking and reporting for BWA and surrounding pipe

resources/analysisTools/qcPipeline/chrom_diff.r

@@ -19,8 +19,14 @@ for(i in 1:nrow(data)){
   v[i] <- sum(data[i,])
 }
 
-pdf(opt$outputFile, height = 10, width = 10)
+# fix for https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows/issues/63
+oldWD = getwd()
+setwd(dirname(opt$outputFile))
+tmpFileName=basename(tempfile(pattern = "DiffChroms_", fileext = ".tmp"))
 
+pdf(tmpFileName, height = 10, width = 10)
 barplot(v, names.arg = rownames(data), col = rainbow(nrow(data)),ylab = "# reads", xlab = "Chromosome", main = plot_title)
-
 dev.off()
+
+file.rename(tmpFileName, opt$outputFile)
+setwd(oldWD)