Synthesis fixer panic (#210)

* Updated synthesisFixer to not use SQL.

* Add comment to go to fixcdssimple

* Added developer docs

* Removed need for magic number

* increase code coverage to 100%

* Fixed if suggestion for fix is larger than the sequence itself

* Added 2 different fixes for particular sequence

Author: Koeng101

synthesis/synthesis.go

@@ -67,13 +67,7 @@ func RemoveSequence(sequencesToRemove []string, reason string) func(string, chan
 				for _, location := range locations {
 					codonLength := 3
 					position := location[0] / codonLength
-					leftover := location[0] % codonLength
-					switch {
-					case leftover == 0:
-						c <- DnaSuggestion{position, (location[1] / codonLength), "NA", 1, reason}
-					case leftover != 0:
-						c <- DnaSuggestion{position, (location[1] / codonLength) - 1, "NA", 1, reason}
-					}
+					c <- DnaSuggestion{position, (location[1] / codonLength) - 1, "NA", 1, reason}
 				}
 			}
 		}
@@ -327,7 +321,7 @@ func FixCds(sequence string, codontable codon.Table, problematicSequenceFuncs []
 
 			// For each suggestion, get a list of potential changes that could fix the problem.
 			var potentialChanges []Change
-			for positionSelector := suggestion.Start; positionSelector <= suggestion.End; positionSelector++ {
+			for positionSelector := suggestion.Start; positionSelector <= suggestion.End && positionSelector < len(historicalMap); positionSelector++ {
 				codonList := historicalMap[positionSelector]
 				lastCodon := codonList[len(codonList)-1]
 				unavailableCodons := make(map[string]bool)

synthesis/synthesis_test.go

@@ -226,3 +226,15 @@ func TestBadCodonTable(t *testing.T) {
 		t.Errorf("TestBadCodonTable should fail with 'incomplete codon table'")
 	}
 }
+
+func TestPanicIndex(t *testing.T) {
+	// lastCodon := codonList[len(codonList)-1] used to fail here with a panic
+	// panic: runtime error: index out of range [-1]
+	// This was because there is a BbsI at the end of the gene and sometimes a
+	// synthesis fix would be requested at 825, out of the sequence range.
+
+	codonTable := codon.ReadCodonJSON(dataDir + "freqB.json")
+	gene := "ATGTCCGAAAAGAATCTGGAGCACAACCACGGTATCATCAAGGGTATCGATATTGCAGCGGAGGTGCGTAAAGACTTCCTGGAGTACAGCATGAGCGTCATCGTGAGCCGCGCACTGCCGGACCTGAAAGACGGTCTGAAACCGGTTCACCGTCGTATTATCTATGCGATGAACGACCTGGGTATCACCGCGGATAAGCCGCACAAGAAGAGCGCGCGTATCGTCGGTGAAGTTATTGGCAAGTATCACCCGCATGGTGACACCGCAGTTTATGATAGCATGGTTCGTATGGCGCAAGATTTTAGCTACCGCTATCCGCTGGTTGACGGCCACGGTAACTTTGGTAGCATCGACGGTGATGGCGCGGCGGCCATGCGTTACACCGAGGCGCGTTTGGCAAAAGTGTCCAATTTTATTATCAAGGACATCGATATGAATACCGTGCCGTTCGTGGACAACTACGACGCAAGCGAGCGTGAACCGGCTTACCTGACGGGCTATTTCCCGAATCTGCTGGCAAATGGTGCAATGGGTATCGCGGTCGGTATGGCTACCAGCATCCCGCCGCATAATCTGCGTGAGGTGATCTCCGCGATTCATGCATTTATCGATAACAAAGATATCACCATCGATGAGATCCTGGACAATCATATTATGGGTCCGGATTTCCCGACCGGTGCTCTGATGACCAACGGTATTCGTATGCGTGAGGGTTACAAAACGGGTCGCGGTGCGGTGACCATCCGCGCTAAAGTCGCACTGGAAGAGAATGATCGCCATGCGCGCTTCATCATTACGGAGATTCCGTATCAGACCAACAAGGCGAAACTGATTGAGCGCATCGCAGAGCTGGTCAAGACGAAGCAGCTGGAAGGTATCAGCGACATTCGTGACGAGAGCAATTATGAAGGTATTCGCATCGTTATCGAGCTGCGTCGCGACAGCAATCCGGACGTGGTCCTGAGCAAGCTGTACAAATTTACCAACTTGCAAACCACGTATAGCTTGAACCTGCTGAGCCTGCACAATAATATTCCGGTTCTGCTGGACCTGAAAAGCATCATCAAACACTACGTCGACTTTCAGATCAACGTTATTATCAAGCGCAGCATTTTTGAGAAGGATAAGATCGAAAAACGCTTCCACATCCTGGAAGCGCTGGATACCGCGCTGGACAATATCGACGCGATTGTCAACATTCTGCGTAACAGCCCGGAGAGCAACGAGGCTAAAATGAAGCTGACCGAAGCGTTCGGCTTCGATGAAGAACAAAATAAAGCGATCCTGGATATGCGTCTGCAACGTTTGGTCGGTCTGGAACGTGGCAAAATCCAGCAGGAGATGGCGCAGATCAAAGAGCGTATTGACTACCTGACCCTGCTGATTAGCGATGAAACCGAACAGAACAATGTTCTGAAGAACCAGCTGAGCGAAATTGCTGAGAAATTCGGTGACAACCGTCGCACGGAGACGATTGACGAGGGTCTGATGGATATCGAGGATGAGGAACTGATTCCGGACGTGAAGACGATGATTCTGCTGAGCGACGAAGGCTATATTCGTCGTGTGGATCCGGAGGAATTTCGCGTCCAAAAGCGCGGTGGTCGCGGTGTGAGCGTGAACTCCAGCAATGAGGACCCGATTGTTATCGCGACGATGGGTAAGATGCGTGACTGGGTCCTGTTTTTCACGAATAGCGGTAAGGTCTTCCGCACCAAAGCCTACAACATTCGCCAATACAGCCGTACCGCGCGCGGCCTGCCGATCGTGAATTTTCTGAACGGTCTGACCGCGGGCGACAAGATTACCGCGATTCTGCCGCTGCGTAATGTGAAAGAGAAAATGAATTATTTGACCTTTATTACCGAGAAGGGTATGATTAAGAAAACCGATATTAGCCTGTTTGACAATATCAACAAAAACGGTAAAATCGCGATTAACTTGAAAGAGGACGACCAACTGGTGACCGTTTTCGCGACCACGGGCGAGGATACCATCTTTGTGGCAAACAAGAGCGGTAAAGTTATCCGTATTCAGGAAAACATCGTCCGCCCGTTGTCTCGTACGGCATCTGGTGTGAAAGCGATTAAGTTGGACGAGAACGATGTGGTGGTGGGTGCAGTTACGAGCTTCGGTATTGAGAACATTACGACCATTTCCTCCAAGGGTAGCTTCAAAAAGACGAACATCGATGAGTATCGTATCAGCGGCCGTAATGGTAAAGGCATCAAAGTCATGAATCTGAACGAAAAGACCGGTGATTTCAAAAGCATCATTGCGGCACGCGAAACCGATCTGGTTTGTATTATTAGCACGGACGGCAATCTGATTAAGACCAAAGCGAGCGATATCCCGGTGCTGGGCCGTGCGGCTGCCGGCGTGCGTGGTATTCGCCTGTCCGAGGGTAATAAGATTCAGGCCGTTATGCTGGAGTACCGTAAACACGGTGAAGAGAACCAGGAATTCGAGGAAGAC"
+	_, _, _ = FixCdsSimple(gene, codonTable, []string{"GAAGAC", "GGTCTC", "GCGATG", "CGTCTC", "GCTCTTC", "CACCTGC", "CGTCTC"})
+
+}