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tseemann / nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
GNU General Public License v2.0
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Resistome report #30

Closed kwongj closed 6 years ago

kwongj commented 9 years ago

Do ticks represent 100% identity AND full length match?

tseemann commented 9 years ago

It seems the answer is no.

According to the code the green tick actually only looks at COVERAGE=100 where it is defined as below:

COVERAGE     100 * ($hit{length}-$hit{gaps}) / $hit{slen}),
IDENTITY         $hit{pident},
tseemann commented 7 years ago

Should we change this behaviour?

tseemann commented 6 years ago

It seems ticks are ONE HIT, with >95% COV. (no ID limit) Orange ? is everything else except no hits which is red cross.

        $hit = @hits == 1 && int($hits[0]->{'%COVERAGE'}) >= 95
             ? $self->pass_fail( +1 )
             : $self->pass_fail( 0, join(' + ', map { int($_->{'%COVERAGE'}).'%' } @hits) );

Should this be changed?

tseemann commented 6 years ago

I've now added a legend to help clarify:

image