def parse_download_args()

in app/source/dragen/src/dragen_qs.py [0:0]

• 58 lines of code
• 25 McCabe index (conditional complexity)

    def parse_download_args(self):
        # -r or --reference: S3 URL for reference HT
        opt_no = find_arg_in_list(self.orig_args, '-r', '--ref-dir')
        if opt_no >= 0:
            self.ref_s3_url = self.orig_args[opt_no + 1]
            self.ref_s3_index = opt_no + 1

        # --output-directory: S3 URL for output location
        opt_no = find_arg_in_list(self.orig_args, '--output-directory')
        if opt_no >= 0:
            self.output_s3_url = self.orig_args[opt_no + 1]
            self.output_s3_index = opt_no + 1

        # --fastq-list: URL (http or s3) for fastq list CSV file
        opt_no = find_arg_in_list(self.orig_args, '--fastq-list')
        if opt_no >= 0:
            self.fastq_list_url = self.orig_args[opt_no + 1]
            self.fastq_list_index = opt_no + 1

        # --tumor-fastq-list: URL (http or s3) for tumor fastq list CSV file
        opt_no = find_arg_in_list(self.orig_args, '--tumor-fastq-list')
        if opt_no >= 0:
            self.tumor_fastq_list_url = self.orig_args[opt_no + 1]
            self.tumor_fastq_list_index = opt_no + 1


        # --vc-target-bed: URL for the VC target bed
        opt_no = find_arg_in_list(self.orig_args, '--vc-target-bed')
        if opt_no >= 0:
            self.vc_tgt_bed_url = self.orig_args[opt_no + 1]
            self.vc_tgt_bed_index = opt_no + 1

        # --vc-depth-intervals-bed: URL for the VC depth intervals
        opt_no = find_arg_in_list(self.orig_args, '--vc-depth-intervals-bed')
        if opt_no >= 0:
            self.vc_depth_url = self.orig_args[opt_no + 1]
            self.vc_depth_index = opt_no + 1

        # --cnv-normals-list : URL for CNV normals list
        opt_no = find_arg_in_list(self.orig_args, '--cnv-normals-list')
        if opt_no >= 0:
            self.cnv_normals_list_url = self.orig_args[opt_no + 1]
            self.cnv_normals_index = opt_no + 1

        opt_no = find_arg_in_list(self.orig_args, '--cnv-target-bed')
        if opt_no >= 0:
            self.cnv_target_bed_url = self.orig_args[opt_no + 1]
            self.cnv_target_index = opt_no + 1

        opt_no = find_arg_in_list(self.orig_args, '--dbsnp')
        if opt_no >= 0:
            self.dbsnp_url = self.orig_args[opt_no + 1]
            self.dbsnp_index = opt_no + 1

        opt_no = find_arg_in_list(self.orig_args, '--cosmic')
        if opt_no >= 0:
            self.cosmic_url = self.orig_args[opt_no + 1]
            self.cosmic_index = opt_no + 1

        opt_no = find_arg_in_list(self.orig_args, '--qc-cross-cont-vcf')
        if opt_no >= 0:
            self.qc_cross_cont_vcf_url = self.orig_args[opt_no + 1]
            self.qc_cross_cont_vcf_index = opt_no + 1

        opt_no = find_arg_in_list(self.orig_args, '--qc-coverage-region-1')
        if opt_no >= 0:
            self.qc_coverage_region_1_url = self.orig_args[opt_no + 1]
            self.qc_coverage_region_1_index = opt_no + 1

        opt_no = find_arg_in_list(self.orig_args, '--qc-coverage-region-2')
        if opt_no >= 0:
            self.qc_coverage_region_2_url = self.orig_args[opt_no + 1]
            self.qc_coverage_region_2_index = opt_no + 1

        opt_no = find_arg_in_list(self.orig_args, '--qc-coverage-region-3')
        if opt_no >= 0:
            self.qc_coverage_region_3_url = self.orig_args[opt_no + 1]
            self.qc_coverage_region_3_index = opt_no + 1

        return