def mergeBAMFiles(infiles, outfile):
'''Merge reads from the same library, run on different lanes '''
if len(infiles) == 1:
P.clone(infiles[0], outfile)
P.clone(infiles[0] + ".bai", outfile + ".bai")
return
infiles = " ".join(infiles)
statement = ''' samtools merge %(outfile)s %(infiles)s >& %(outfile)s.log'''
P.run()
def buildGeneSet(infile, outfile):
''' link to the geneset provided'''
P.clone(os.path.abspath(infile), os.path.abspath(outfile))
