Add option to report all matched schemes

[hmontenegro]

It would be nice to have an option to report all matched schemes above the score, instead of reporting just the best one.

Case in point: for an isolate genome which is not truly an isolate, the output is:

contigs.fa  abaumannii_2    15  Pas_cpn60(6)    Pas_fusA(6) Pas_gltA(8) Pas_pyrG(2) Pas_recA(3) Pas_rplB(5) Pas_rpoB(4)

However, --debug shows:

$VAR1 = [
          'abaumannii_2',
          15,
          '6/6/8/2/3/5/4',
          100
        ];
$VAR2 = [
          'bcereus',
          1280,
          '33/8/13/19/8/17/201',
          100
        ];
$VAR3 = [
          '-',
          '-',
          '-/-/-/-/-/-/-',
          0
        ];

Showing multiple matching schemes would allow quick screening of contaminated isolates. The default for this option would be to report the best match, so no changes to current behaviour.

[tseemann]

What would you expect to happen when multiple genome files were provided?

[hmontenegro]

hmm, didn't think about it. So far, I have used mlst for one genome at a time.

When multiple genome files were provided, I would expect each genome would be processed in turn, and get one or more schemes. So, in a scenario with three genomes, two good isolates and one a bad isolate, calling:

mlst genome1.fa genome2.fa genome3.fa

Would result in:

genome1.fa  abaumannii_2    15  Pas_cpn60(6)    Pas_fusA(6) Pas_gltA(8) Pas_pyrG(2) Pas_recA(3) Pas_rplB(5) Pas_rpoB(4)
genome2.fa  bcereus 1280    glp(33) gmk(8)  ilv(13) pta(19) pur(8)  pyc(17) tpi(201)
genome3.fa  abaumannii_2    15  Pas_cpn60(6)    Pas_fusA(6) Pas_gltA(8) Pas_pyrG(2) Pas_recA(3) Pas_rplB(5) Pas_rpoB(4)
genome3.fa  bcereus 1280    glp(33) gmk(8)  ilv(13) pta(19) pur(8)  pyc(17) tpi(201)