def mergeBamsByRep(infiles, outfile):
'''Merge all replicates of the same experiment together'''
statement = '''samtools merge -f %(outfile)s %(infiles)s;
checkpoint;
samtools index %(outfile)s'''
if len(infiles) == 1:
IOTools.cloneFile(infiles[0], outfile)
IOTools.cloneFile(infiles[0]+".bai", outfile+".bai")
else:
infiles = " ".join(infiles)
P.run()
