def doScaffolding(self, outputDir, assembly, pool):
for lib in pool.libs:
lib.mergedFile = outputDir + lib.libName + "Merged.fastq"
if os.path.exists(lib.mergedFile) == False or Configuration.instance.getGlobalOption("overwrite") == 1:
FastqUtils.mergeFastqFiles(lib.forward, lib.reversed, lib.mergedFile)
scarpaProcesser = ScarpaProcess(outputDir, contigs=assembly, libs=pool.libs)
scarpaContigs = scarpaProcesser.execute()
libInfo = scarpaProcesser.libInfo
mergedFiles = []
for lib in pool.libs:
mergedFiles.append(lib.mergedFile)
samFile = BowtieOne(outputDir, contigs=scarpaContigs, mergedFiles=mergedFiles).execute()
mapFile = ScarpaParser(outputDir, samFile=samFile).execute()
self.scaffolds = ScarpaCommand(outputDir, libInfo = libInfo, contigs = scarpaContigs, mappedFile=mapFile).execute()
return self.scaffolds
