Task: expandflag

martinghunt edited this page Jun 27, 2017 · 1 revision

Task: expandflag

This takes a report file (made by ariba run), and expands the flag column from a number into a string showing the meaning of the flag. For example flag 27, which has this meaning:

[X] assembled
[X] assembled_into_one_contig
[ ] region_assembled_twice
[X] complete_gene
[X] unique_contig
[ ] scaffold_graph_bad
[ ] assembly_fail
[ ] variants_suggest_collapsed_repeat
[ ] hit_both_strands
[ ] has_variant
[ ] ref_seq_choose_fail

becomes assembled,assembled_into_one_contig,complete_gene,unique_contig instead of the number 27.

Run it like this:

ariba expandflag in.report.tsv out.report.tsv

The output file will be identical to the input file, except for the flag column.

You can’t perform that action at this time.
You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session.
Press h to open a hovercard with more details.