usage: add_matesequence [-h] -a FILE_TO_ANNOTATE -s ANNOTATE_SOURE -o OUTPUT_PATH [--version] Annotate reads with Mate Sequence in tag field optional arguments: -h, --help show this help message and exit -a FILE_TO_ANNOTATE, --file_to_annotate FILE_TO_ANNOTATE Annotate reads in this file with their mate sequence -s ANNOTATE_SOURE, --annotate_soure ANNOTATE_SOURE Use this file to find the mate sequence (can be same file as file_to_annotate) -o OUTPUT_PATH, --output_path OUTPUT_PATH Write resulting BAM file to this path --version show program's version number and exit