remove restriction of 10 alleles max in multiallelic sites (#11)

* remove restriction of 10 alleles max in multiallelic sites

* fix haploid with allele > 9, add test

* improve strictness of bi-allelic check, add clarifying comments

* rune comparison is 15-20x faster than string, even with casts

* add go.mod and go.sum

benchmarks_test.go

@@ -0,0 +1,113 @@
+package main
+
+import (
+	"testing"
+)
+
+// Benchmark for comparing a rune element with a rune variable
+func BenchmarkRuneEquality(b *testing.B) {
+	// Sample rune slice and a rune variable to compare with
+	data := []rune{'a', 'b', 'c'}
+	compareRune := 'a'
+
+	b.ResetTimer() // Reset the timer to exclude setup time
+	for i := 0; i < b.N; i++ {
+		for _, r := range data {
+			if r == compareRune {
+				// Perform some action if equal
+			}
+		}
+	}
+}
+
+// Benchmark for comparing a rune element cast to a string with a string variable
+func BenchmarkStringEquality(b *testing.B) {
+	// Sample rune slice and a string variable to compare with
+	data := []rune{'a', 'b', 'c'}
+	compareString := "a"
+
+	b.ResetTimer() // Reset the timer to exclude setup time
+	for i := 0; i < b.N; i++ {
+		for _, r := range data {
+			if string(r) == compareString {
+				// Perform some action if equal
+			}
+		}
+	}
+}
+
+func BenchmarkStringToRuneEquality(b *testing.B) {
+	// Sample rune slice and a string variable to compare with
+	data := []string{"a", "b", "c"}
+	compareRune := 'a'
+
+	b.ResetTimer() // Reset the timer to exclude setup time
+	for i := 0; i < b.N; i++ {
+		for _, r := range data {
+			if rune(r[0]) == compareRune {
+				// Perform some action if equal
+			}
+		}
+	}
+}
+
+func BenchmarkStringToStringEquality(b *testing.B) {
+	// Sample rune slice and a string variable to compare with
+	data := []string{"a", "b", "c"}
+	compareString := "a"
+
+	b.ResetTimer() // Reset the timer to exclude setup time
+	for i := 0; i < b.N; i++ {
+		for _, r := range data {
+			if string(r[0]) == compareString {
+				// Perform some action if equal
+			}
+		}
+	}
+}
+
+func BenchmarkGenotypeToStringEquality(b *testing.B) {
+	// Sample rune slice and a string variable to compare with
+	data := []string{"0|1", "1|0", "0|1"}
+	compareString := "0"
+
+	b.ResetTimer() // Reset the timer to exclude setup time
+	for i := 0; i < b.N; i++ {
+		for _, r := range data {
+			if string(r[0]) == compareString {
+				// Perform some action if equal
+			}
+		}
+	}
+}
+
+func BenchmarkGenotypeToRuneEquality(b *testing.B) {
+	// Sample rune slice and a string variable to compare with
+	data := []string{"0|1", "1|0", "0|1"}
+	compareString := "0"
+
+	b.ResetTimer() // Reset the timer to exclude setup time
+	for i := 0; i < b.N; i++ {
+		for _, r := range data {
+			if rune(r[0]) == rune(compareString[0]) {
+				// Perform some action if equal
+			}
+		}
+	}
+}
+
+func BenchmarkGenotypeToRuneEqualityWithLengthTest(b *testing.B) {
+	data := []string{"0|1", "1|0", "0|1"}
+	compareString := "0"
+
+	b.ResetTimer() // Reset the timer to exclude setup time
+	for i := 0; i < b.N; i++ {
+		if len(compareString) == 1 {
+			for _, r := range data {
+				if rune(r[0]) == rune(compareString[0]) {
+					// Perform some action if equal
+				}
+			}
+		}
+	}
+}

go.mod

@@ -0,0 +1,5 @@
+module github.com/bystrogenomics/bystro-vcf
+
+go 1.20
+
+require github.com/akotlar/bystro-utils v0.0.0-20180921004542-b5183a523f20

go.sum

@@ -0,0 +1,2 @@
+github.com/akotlar/bystro-utils v0.0.0-20180921004542-b5183a523f20 h1:DTPJA8O7qs7Dc+YRg9wZusDy/SoVHqn9udRQlr+TSFA=
+github.com/akotlar/bystro-utils v0.0.0-20180921004542-b5183a523f20/go.mod h1:BHUTiQAFM7OSW8+09I/OwWMhgbsonqQ6J8jTlnpOPnk=