sys.stderr.write(bam+' file should be linked to a library named '+lib_name+'.\n')
sys.exit(1)
ifself.args["count_matrix"]:
fh=open(self.args["count_matrix"])
line=fh.readline()
matrix_libs=[]
parts=line.rstrip().split("\t")
matrix_libs=parts[1:]
forlib_nameinmatrix_libs:
ifself.get_library_from_name(lib_name)==None:
sys.stderr.write('Library '+lib_name+' defined at the first line of the matrix file has not been defined (see --library option to define a library)\n')
sys.exit(1)
ifself.args["variant"]["file"]:
reader=VCFReader(self.args["variant"]["file"])
forfullpath,samplenameinreader.samples_name:
ifself.get_library_from_name(lib_name)==None:
sys.stderr.write('Library '+samplename+' defined in the vcf file has not been defined (see --library option to define a library)\n')