usage: readtagger [-h] -t TAG_FILE -a ANNOTATE_WITH [ANNOTATE_WITH ...] -o OUTPUT_FILE [-d] [-dp] [-k] [-wd WRITE_DISCARDED] [-wv WRITE_VERIFIED] [--version] Tag reads in an alignment file based on other alignment files optional arguments: -h, --help show this help message and exit -t TAG_FILE, --tag_file TAG_FILE Tag reads in this file. (default: None) -a ANNOTATE_WITH [ANNOTATE_WITH ...], --annotate_with ANNOTATE_WITH [ANNOTATE_WITH ...] Tag reads in readfile if reads are aligned in these files.Append `:A:B` to tag first letter of tag describing read as A, and first letter of tag describing the mate as B (default: None) -o OUTPUT_FILE, --output_file OUTPUT_FILE Write bam file to this path (default: None) -d, --allow_dovetailing Sets the proper pair flag (0x0002) to true if reads dovetail [reads reach into or surpass the mate sequence]. (default: False) -dp, --discard_if_proper_pair Discard an alternative flag if the current read is in a proper pair. (default: False) -k, --keep_suboptimal_alternate_tags By default cigarstrings of the alternative tags are compared and alternates that are not explaining the current cigar strings are discarded. Use this option to keep the alternative tags (effectively restoring the behaviour of readtagger < 0.1.4) (default: False) -wd WRITE_DISCARDED, --write_discarded WRITE_DISCARDED Write discarded reads into separate file (default: False) -wv WRITE_VERIFIED, --write_verified WRITE_VERIFIED Write verified reads into separate file (default: False) --version show program's version number and exit