Merge branch 'feature-a/3910-avoir-des-germline-de-poulet' into 'dev'

Resolve "Avoir des germline de poulet"

Closes #3910

See merge request !478

algo/tests/data/specie_gallus-gallus.fa

+# each of these sequences are compatible with allele 01 & 02.
+# So a warning will be called
+>IGLV1-1*01 0//2 IGLJ*01
+CTGGGGTCCAAGCCGACGACGAGGCTGTCTATTACTGTGGGAGTGCAGACAGCAGCAGTACTGCTGGTATATTTGGGGCCGGGACAACCCTGACCGTCCTAGGCCAGCCCAAGGTGGCCCCCACCATCACCCTCTTCCCA
+>IGLV1-1*01 0/C/6 IGLJ*01
+GGTCCAAGCCGACGACGAGGCTGTCTATTACTGTGGGAGTGCAGACAGCAGCAGTACTGCTGCATTTGGGGCCGGGACAACCCTGACCGTCCTAGGCCAGCCCAAGGTGGCCCCCACCATCACCCTCTTCCCACCGTCAAAG
+>IGLV1-4*01 0//6 IGLJ*01
+GCCGACGACGAGGCTGTCTATTACTGTGGGAGTGCAGACAGCAGCTATGTTGGTATATTTGGGGCCGGGACAACCCTGACCGTCCTAGGCCAGCCCAAGGTGGCCCCCACCATCACCCTCTTCCCACCGTCAAAGGA
\ No newline at end of file

algo/tests/should-get-tests/species-gallus-gallus.should

+!LAUNCH: $VIDJIL_DIR/$EXEC -3 -c designations -g $VIDJIL_DIR/germline/gallus-gallus.g $VIDJIL_DATA/specie_gallus-gallus.fa
+
+# each sequence here can be allele *01 or *02.
+
+$ First clone is correctly found
+1:IGLV1-1.01 0//2 IGLJ.01
+
+$ Second clone is correctly found
+1:IGLV1-1.01 0/C/6 IGLJ.01
+
+$ Third clone is correctly found
+1:IGLV1-4.01 0//6 IGLJ.01
+
+

germline/gallus-gallus.g

@@ -29,7 +29,7 @@
             "follows": "IGH",
             "recombinations": [ {
                 "5": ["IGHD+up.fa"],
-                "3": ["IGHJ+down.fa"]
+                "3": ["IGHJ.fa"]
             } ],
             "parameters": {
                 "seed": "12s"