tests: tdd, update test, actual start V positions and codes

algo/tests/data/productive_stop_before_V.fa

-# These sequences have stop codon before the start of the V gene
-# result should be productive
+# These two recombinations start before the start of the V gene, including a stop codon in that zone.
+# They should be productive
 
->IGHV1-69*06 2/AACCCCCAACAAAGC/4 IGHD3-3*01 9/CCCATAAGTACCGT/1 IGHJ6*02 [IGH]
-CTGGAGGTTCCTCTTTGTGGTGGCAGCAGCTACAGGTAAGGGGCTTCCTAGTCCTAAGGCTGAGGAAGGGATCCTGGTTTAGTTAAAGAGGATTTTATTCACCCCTGTGTCCTGTCCACAGGTGTCCAGTCCCAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAGGGATCATCCCTATCTTTGGTACAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAAACCCCCAACAAAGCTACGATTTTTGGAGTGGTCCCATAAGTACCGTTTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAGGTAAG
+# start of the V gene @133
+# end of the J gene @534
+>132/0 IGHV1-69*06 2/AACCCCCAACAAAGC/4 IGHD3-3*01 9/CCCATAAGTACCGT/1 IGHJ6*02 40/GGTAAG [IGH]
+CTGGAGGTTCCTCTTTGTGGTGGCAGCAGCTACAGGTAAGGGGCTTCCTAGTCCTAAGGCTGAGGAAGGGATCCTGGTTTAGTTAAAGAGGATTTTATTCACCCCTGTGTCCTGTCCACAGGTGTCCAGTCC
+CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAGGGATCATCCCTATCTTTGGTACAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAAACCCCCAACAAAGCTACGATTTTTGGAGTGGTCCCATAAGTACCGTTTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG
+GTAAG
+
+# start of the V gene @146
+>145/0 IGHV3-74*01 0/GACCG/6 IGHD1-7*01 0/GC/10 IGHJ4*02 [IGH]
+AGCTGGGTTTTCCTTGTTGCTATTTTAAAAGGTGATTCATGGAGAATTGGAGATGTGGAGTGTGAATGGACATGGGTGAGATAAGCAGTGGATGTGTGTGGCAGTTTCTGACCAGGGTGTCTCTGTGTTTGCAGGTGTCTCGTGT
+GAGGTGCTTCTGGTGGAGTCCGGGGGAGGCTTAGTTAAGGCGGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAATTACTGGATGCACTGGGTCCGCCAAGTTCCAGGGAAGGGCCTGGAGTGGGTCTCACGTATTAACAGCGATGGGAGCGCCATAAGGTACGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGGACACACTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCTGTTTATTATTGTGCAAGAGAGACCGACTGGAATTACGCCTACTGGGGCCAGGGAACCCTGGTC
+# actual sequence was continuing after J
+# ... ACCGTCTCCT CAGGTAAG
 
->IGHV3-74*01 0/GACCG/6 IGHD1-7*01 0/GC/10 IGHJ4*02 [IGH]
-AGCTGGGTTTTCCTTGTTGCTATTTTAAAAGGTGATTCATGGAGAATTGGAGATGTGGAGTGTGAATGGACATGGGTGAGATAAGCAGTGGATGTGTGTGGCAGTTTCTGACCAGGGTGTCTCTGTGTTTGCAGGTGTCTCGTGTGAGGTGCTTCTGGTGGAGTCCGGGGGAGGCTTAGTTAAGGCGGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAATTACTGGATGCACTGGGTCCGCCAAGTTCCAGGGAAGGGCCTGGAGTGGGTCTCACGTATTAACAGCGATGGGAGCGCCATAAGGTACGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGGACACACTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCTGTTTATTATTGTGCAAGAGAGACCGACTGGAATTACGCCTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGGTAAG

algo/tests/should-get-tests/productive_stop_before_V.should

@@ -2,15 +2,27 @@
 !OUTPUT_FILE: out/productive_stop_before_V.vidjil
 
 $ first clone name
-1: "IGHV1-69*06 2/AACCCCCAACAAAGC/4 IGHD3-3*01 9/CCCATAAGTACCGT/1 IGHJ6*02"
+1: "IGHV1-69.06 2/AACCCCCAACAAAGC/4 IGHD3-3.01 9/CCCATAAGTACCGT/1 IGHJ6.02"
 $ second clone name
-1: "IGHV3-74*01 0/GACCG/6 IGHD1-7*01 0/GC/10 IGHJ4*02"
+1: "IGHV3-74.01 0/GACCG/6 IGHD1-7.01 0/GC/10 IGHJ4.02"
 
-$ We should get 6 start position in vidjil (2 by segments)
-6: "start"
+# There are 10 = 2x5 segments (V, D, J, cdr3 and junction)
 
-$ We should get 6 stop position in vidjil (2 by segments)
-6: "stop"
+$ Correct number of start positions
+10: "start"
+
+$ Correct start position of IGHV1-69*06
+1: "start": 133
+
+$ Correct stop position of IGHJ6*02
+1: "stop": 534
+
+$ Correct start position of IGHV3-74*01
+1: "start": 146
+
+$ Correct number of stop positions (10-1, no stop positions for J on the second sequence)
+9: "stop"
+
+$ The two sequences are productive
+f2: "productive": true
 
-$ But only one productive
-2: "productive": true