diff --git a/bin/abricate b/bin/abricate index 80df173..c02c299 100755 --- a/bin/abricate +++ b/bin/abricate @@ -21,7 +21,7 @@ my $URL = 'https://github.com/tseemann/abricate'; #.............................................................................. # Command line options -my(@Options, $debug, $quiet, $setupdb, $list, $summary, $check, +my(@Options, $debug, $quiet, $setupdb, $list, $summary, $identity, $check, $datadir, $db, $minid, $mincov, $threads, $noheader, $csv, $nopath, $fofn); setOptions(); @@ -68,6 +68,11 @@ if ($fofn) { @ARGV = @filenames; } +if ($identity) { + $FIELD = '%IDENTITY'; + msg("Using %IDENTITY for the summary table instead of %COVERAGE"); +} + if ($summary) { @ARGV >= 1 or err("--summary needs >=1 abricate output files"); summary_table( @ARGV ); @@ -459,6 +464,7 @@ sub setOptions { {OPT=>"mincov=f", VAR=>\$mincov, DEFAULT=>80, DESC=>"Minimum DNA %coverage"}, "MODE", {OPT=>"summary!", VAR=>\$summary, DESC=>"Summarize multiple reports into a table"}, + {OPT=>"identity!", VAR=>\$identity, DESC=>"Use %IDENTITY instead of %COVERAGE in summary table"}, ); @ARGV or usage(1);