Issue #2 - use ? for novel alleles

.travis.yml

@@ -30,3 +30,4 @@ script:
     - "! (legsta --quiet test/NC_006368.fna |& grep Loaded)"
     - "legsta /dev/null 2>&1 | grep ERROR"
     - legsta test/CR628336.1.gbk.gz | grep -P "1\t1\t4\t3\t1\t1\t1\t1"
+    - legsta test/FJBS01000000.fna.bz2 | grep -F '?'

README.md

@@ -41,15 +41,20 @@ The files may also be compressed with gzip, bzip2 or zip.
 ## Output
 
 Output is a TSV file (or CSV if `--csv` is used).
+Alleles with no _in silico_ product are denoted `-`
+and novel alleles listed using `?`.
+
 ```
 % cd legsta/test
-% ../bin/legsta NC_006368.fna NC_018140.fna CR628336.1.gbk.gz
+% ../bin/legsta NC_006368.fna NC_018140.fna CR628336.1.gbk.gz missing_flaA.fna FJBS01000000.fna.bz2
 
 
-FILE  		     SBT     flaA    pilE    asd     mip     mompS   proA    neuA
-NC_006368.fna        1       1       4       3       1       1       1       1
-NC_018140.fna        734     2       6       17      1       1       8       11
-CR628336.1.gbk.gz    1       1       4       3       1       1       1       1
+FILE  		       SBT     flaA    pilE    asd     mip     mompS   proA    neuA
+NC_006368.fna          1       1       4       3       1       1       1       1
+NC_018140.fna          734     2       6       17      1       1       8       11
+CR628336.1.gbk.gz      1       1       4       3       1       1       1       1
+missing_flaA.fna       -       -       14      16      25      7       13      206
+FJBS01000000.fna.bz2   -       3       10      1       3       14      9       ?
 
 ```
 

bin/legsta

@@ -9,13 +9,14 @@ use Cwd 'abs_path';
 #..............................................................................
 # Globals
 
-my $VERSION = "0.5.0";
+my $VERSION = "0.5.1";
 my $URL = "https://github.com/tseemann/legsta";
 my $OUTSEP = "\t";
 my $ISPCR = "isPcr";
 my $ISPCR_OPT = "-minPerfect=5 -tileSize=6 -maxSize=1200 -stepSize=5";
 my $SEP = "/";
 my $UNK = "-";
+my $NOVEL = "?";
 
 #..............................................................................
 # Command line options
@@ -86,7 +87,7 @@ for my $fasta (@ARGV) {
   # Determine the allele profile
   my @profile;
   for my $g (@gene) {
-    my $num = $UNK;
+    my $num = $NOVEL;
     if (my $hit = $amp->{$g}) {
       msg("Scanning $g database") if $debug;
       # Look for exact substring matches in linear search (db is small)
@@ -97,6 +98,9 @@ for my $fasta (@ARGV) {
         }
       }
     }
+    else {
+      $num = $UNK;
+    }
     msg("Allele $g => $num") if $debug;
     push @profile, $num;
   }