def index(uuid, analysis_ready_bam_list_path, engine, logger): with open (analysis_ready_bam_list_path) as f: analysis_ready_bam_path = f.read().splitlines() for path in analysis_ready_bam_path: analysis_ready_bai_path = path + '.bai' if os.path.isfile(analysis_ready_bai_path): logger.info('analysis_ready_bai_path=%s' % analysis_ready_bai_path) else: analysis_ready_bai_path = bam_util.samtools_bam_index(uuid, path, engine, logger)
def index(uuid, harmonized_bam_list_path, engine, logger): with open(harmonized_bam_list_path) as f: harmonized_bam_path = f.read().splitlines() for path in harmonized_bam_path: harmonized_bai_path = path + '.bai' if os.path.isfile(harmonized_bai_path): logger.info('harmonized_bai_path=%s' % harmonized_bai_path) else: harmonized_bai_path = bam_util.samtools_bam_index(uuid, path, engine, logger)