(top, bgVec)

(self, run_name, bowtiebuild, hla1fasta, mapopt, locus_list, hla_class, hla_classification, length_dict)

(self, sam, run_name, fq1, fq2, bowtiebuild, iteration, mapopt)

(self, sam, medians, output, medianflag, locus_list, hla_class, readcount, readspergroup, hla_classification)

(self, map, sam, readcount)

(self, hlafasta, class1_list)

(self, file)

(self, run_name, removeList)

(self, finalAlleles, finaloutput4digit, locus_list)

(self, run_name)

(dbmhc, dbmhc_file)

(self, run_name, map, locus_list)

(self, run_name, map, fourdigits1_dict)

(dbmhc, infile, bgVec, run_name)

(infile, bgVec, run_name)

(self, locus_list, length_dict, map, run_name)

(self, locus, finaloutput)

(infile)

()

(self, entries, readspergroup_dict, output, allele_dict, HLAclass, locus_list)

(self, output1, output2, finaloutput, locus_list)

(self)

(self, run_name, fq1, fq2, trim3, threads)

(infile, bgVec, run_name, hla_class, hla_classification)

(freq_dict)