Fix PCR bug (issue #279). (#378)

bebop · Sep 26, 2023 · 41a9515 · 41a9515
1 parent d2ae0de
commit 41a9515
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Showing 2 changed files with 18 additions and 1 deletion.
diff --git a/primers/pcr/pcr.go b/primers/pcr/pcr.go
@@ -178,7 +178,7 @@ func Simulate(sequences []string, targetTm float64, circular bool, primerList []
 
 func generatePcrFragments(sequence string, forwardLocation int, reverseLocation int, forwardPrimerIndxs []int, reversePrimerIndxs []int, minimalPrimers []string, primerList []string) []string {
 	var pcrFragments []string
-	for forwardPrimerIndex := range forwardPrimerIndxs {
+	for _, forwardPrimerIndex := range forwardPrimerIndxs {
 		minimalPrimer := minimalPrimers[forwardPrimerIndex]
 		fullPrimerForward := primerList[forwardPrimerIndex]
 		for _, reversePrimerIndex := range reversePrimerIndxs {

diff --git a/primers/pcr/pcr_test.go b/primers/pcr/pcr_test.go
@@ -2,6 +2,8 @@ package pcr
 
 import (
 	"testing"
+
+	"github.com/google/go-cmp/cmp"
 )
 
 // gene is a gene for testing PCR
@@ -72,3 +74,18 @@ func TestSimulateConcatemerization(t *testing.T) {
 		t.Errorf("Should have gotten concatemerization")
 	}
 }
+
+// Test to catch bug discovered by @Koeng101, see issue #279.
+func TestIssue279PCRBug(t *testing.T) {
+	gene := "aataattacaccgagataacacatcatggataaaccgatactcaaagattctatgaagctatttgaggcacttggtacgatcaagtcgcgctcaatgtttggtggcttcggacttttcgctgatgaaacgatgtttgcactggttgtgaatgatcaacttcacatacgagcagaccagcaaacttcatctaacttcgagaagcaagggctaaaaccgtacgtttataaaaagcgtggttttccagtcgttactaagtactacgcgatttccgacgacttgtgggaatccagtgaacgcttgatagaagtagcgaagaagtcgttagaacaagccaatttggaaaaaaagcaacaggcaagtagtaagcccgacaggttgaaagacctgcctaacttacgactagcgactgaacgaatgcttaagaaagctggtataaaatcagttgaacaacttgaagagaaaggtgcattgaatgcttacaaagcgatacgtgactctcactccgcaaaagtaagtattgagctactctgggctttagaaggagcgataaacggcacgcactggagcgtcgttcctcaatctcgcagagaagagctggaaaatgcgctttcttaa"
+
+	fragments, err := Simulate([]string{gene}, 55.0, false, []string{"TATATGGTCTCTTCATTTAAGAAAGCGCATTTTCCAGC", "TTATAGGTCTCATACTAATAATTACACCGAGATAACACATCATGG", "CTGCAGGTCGACTCTAG"})
+	if err != nil {
+		t.Fatalf("unexpected error during PCR simulation: %v", err)
+	}
+
+	want := "TTATAGGTCTCATACTAATAATTACACCGAGATAACACATCATGGATAAACCGATACTCAAAGATTCTATGAAGCTATTTGAGGCACTTGGTACGATCAAGTCGCGCTCAATGTTTGGTGGCTTCGGACTTTTCGCTGATGAAACGATGTTTGCACTGGTTGTGAATGATCAACTTCACATACGAGCAGACCAGCAAACTTCATCTAACTTCGAGAAGCAAGGGCTAAAACCGTACGTTTATAAAAAGCGTGGTTTTCCAGTCGTTACTAAGTACTACGCGATTTCCGACGACTTGTGGGAATCCAGTGAACGCTTGATAGAAGTAGCGAAGAAGTCGTTAGAACAAGCCAATTTGGAAAAAAAGCAACAGGCAAGTAGTAAGCCCGACAGGTTGAAAGACCTGCCTAACTTACGACTAGCGACTGAACGAATGCTTAAGAAAGCTGGTATAAAATCAGTTGAACAACTTGAAGAGAAAGGTGCATTGAATGCTTACAAAGCGATACGTGACTCTCACTCCGCAAAAGTAAGTATTGAGCTACTCTGGGCTTTAGAAGGAGCGATAAACGGCACGCACTGGAGCGTCGTTCCTCAATCTCGCAGAGAAGAGCTGGAAAATGCGCTTTCTTAAATGAAGAGACCATATA"
+	if diff := cmp.Diff(fragments[0], want); diff != "" {
+		t.Errorf("incorrect PCR output (-want,+got): %s", diff)
+	}
+}