fix: rand.Seed(xx)

cmd/samConsensus/samConsensus_test.go

@@ -44,7 +44,7 @@ var samConsensusTests = []struct {
 }
 
 func TestSamConsensus(t *testing.T) {
-	rand.Seed(1)
+	rand.New(rand.NewSource(1))
 	var err error
 	var s Settings
 	for _, v := range samConsensusTests {

cmd/simulateDivergentWindowsVcf/simulateDivergentWindowsVcf.go

@@ -33,6 +33,7 @@ func simulateDivergentWindowsVcf(s Settings) {
 	}
 
 	rand.Seed(s.SetSeed)
+
 	var err error
 	var TotalSites []vcf.Vcf = make([]vcf.Vcf, s.NumTotalSites)
 	var windows []Window = make([]Window, s.NumWindows)
@@ -44,8 +45,8 @@ func simulateDivergentWindowsVcf(s Settings) {
 	for i := 0; i < s.NumWindows; i++ {
 		windows[i].Variants = make([]vcf.Vcf, s.NumWindowSites)
 		//Shuffle the vcf records, our subset will be composed to the first entries in the shuffled order.
-		rand.Seed(s.SetSeed * int64(i))
-		rand.Shuffle(len(TotalSites), func(i, j int) { TotalSites[i], TotalSites[j] = TotalSites[j], TotalSites[i] })
+		r := rand.New(rand.NewSource(s.SetSeed * int64(i)))
+		r.Shuffle(len(TotalSites), func(i, j int) { TotalSites[i], TotalSites[j] = TotalSites[j], TotalSites[i] })
 		copy(windows[i].Variants, TotalSites[:s.NumWindowSites]) //keep only as many results as specified
 		windows[i].NumDivergent = countDivergent(windows[i].Variants)
 	}

cmd/simulateEvol/genic.go

@@ -3,13 +3,14 @@
 import (
 	"flag"
 	"fmt"
+	"log"
+	"math/rand"
+	"os"
+
 	"github.com/vertgenlab/gonomics/exception"
 	"github.com/vertgenlab/gonomics/expandedTree"
 	"github.com/vertgenlab/gonomics/fasta"
 	"github.com/vertgenlab/gonomics/simulate"
-	"log"
-	"math/rand"
-	"os"
 )
 
 type GenicSettings struct {
@@ -63,7 +64,7 @@
 
 func Genic(s GenicSettings) {
 	var fastas, leafFastas []fasta.Fasta
-	rand.Seed(s.SetSeed)
+	rand.New(rand.NewSource(s.SetSeed))
 
 	tree, err := expandedTree.ReadTree(s.TreeFile, s.InFile)
 	exception.PanicOnErr(err)

cmd/statCalc/statCalc.go

@@ -6,14 +6,15 @@ package main
 import (
 	"flag"
 	"fmt"
+	"log"
+	"math/rand"
+	"strings"
+
 	"github.com/vertgenlab/gonomics/exception"
 	"github.com/vertgenlab/gonomics/fileio"
 	"github.com/vertgenlab/gonomics/numbers"
 	"github.com/vertgenlab/gonomics/numbers/parse"
 	"github.com/vertgenlab/gonomics/popgen"
-	"log"
-	"math/rand"
-	"strings"
 )
 
 func statCalc(s Settings) {

cmd/wigTools/math.go

@@ -3,16 +3,17 @@ package main
 import (
 	"flag"
 	"fmt"
-	"github.com/vertgenlab/gonomics/bed"
-	"github.com/vertgenlab/gonomics/exception"
-	"github.com/vertgenlab/gonomics/fileio"
-	"github.com/vertgenlab/gonomics/numbers"
-	"github.com/vertgenlab/gonomics/wig"
 	"log"
 	"math"
 	"math/rand"
 	"os"
 	"sort"
+
+	"github.com/vertgenlab/gonomics/bed"
+	"github.com/vertgenlab/gonomics/exception"
+	"github.com/vertgenlab/gonomics/fileio"
+	"github.com/vertgenlab/gonomics/numbers"
+	"github.com/vertgenlab/gonomics/wig"
 )
 
 // MathSettings defines the usage settings for the wigTools math subcommand.
@@ -110,7 +111,7 @@ func parseMathArgs() {
 
 // wigMth performs mathematical operations on input wig format files.
 func wigMath(s MathSettings) {
-	rand.Seed(s.SetSeed)
+	rand.New(rand.NewSource(s.SetSeed))
 	var err error
 	var second map[string]wig.Wig
 	var foundInMap bool

exception/exception.go

@@ -35,7 +35,7 @@
 
 	err := os.Setenv("GODEBUG", strings.Join(variables, ","))
 	PanicOnErr(err)
-	rand.Seed(0)
+	rand.New(rand.NewSource(0))
 }
 
 // PanicOnErr will panic if input error is not nil.

exception/exception_test.go

@@ -0,0 +1,47 @@
+package exception
+
+import (
+	"bytes"
+	"fmt"
+	"log"
+	"os"
+	"strings"
+	"testing"
+)
+
+func TestPanicOnErr(t *testing.T) {
+	defer func() {
+		if r := recover(); r == nil {
+			t.Errorf("PanicOnErr did not panic on error...\n")
+		}
+	}()
+	var err error = fmt.Errorf("Error: panic exception error handling...\n")
+	PanicOnErr(err)
+}
+
+func TestFatalOnErr(t *testing.T) {
+	// Test with no error
+	var buf bytes.Buffer
+	log.SetOutput(&buf)
+	defer func() { log.SetOutput(os.Stderr) }()
+
+	FatalOnErr(nil)
+	if buf.Len() > 0 {
+		t.Errorf("Error: FatalOnErr logged output when no error was provided")
+	}
+
+}
+
+func TestWarningOnErr(t *testing.T) {
+	var buf bytes.Buffer
+	log.SetOutput(&buf)
+	defer func() {
+		log.SetOutput(os.Stderr)
+	}()
+	var warning string = "Warning: warning error handling...\n"
+
+	WarningOnErr(fmt.Errorf(warning))
+	if !strings.Contains(buf.String(), warning) {
+		t.Errorf("Error: WarningOnErr did not log the correct warning message")
+	}
+}

expandedTree/expandedTree.go

@@ -9,9 +9,9 @@ import (
 	"strings"
 
 	"github.com/vertgenlab/gonomics/dna"
+	"github.com/vertgenlab/gonomics/exception"
 	"github.com/vertgenlab/gonomics/fasta"
 	"github.com/vertgenlab/gonomics/fileio"
-	"github.com/vertgenlab/gonomics/exception"
 	"github.com/vertgenlab/gonomics/tree"
 )
 
@@ -26,7 +26,7 @@ type ETree struct {
 	Scrap                 float64
 	Left                  *ETree
 	Right                 *ETree
-	Up                    *ETree         // The immediate ancestral node.
+	Up                    *ETree      // The immediate ancestral node.
 	DescendentBasePresent bool        // True if any descendent nodes have a base, in a specific position
 	BasePresent           bool        // True if this node has a base (A, C, G, T, or N). False if this node has dna.Gap.
 	SubstitutionMatrix    [][]float64 // for custom substitution matrices. This is a 4x4 substitution matrices for nucleotides.

genomeGraph/giraf.go

@@ -2,13 +2,14 @@ package genomeGraph
 
 import (
 	"fmt"
+	"log"
+	"math/rand"
+
 	"github.com/vertgenlab/gonomics/cigar"
 	"github.com/vertgenlab/gonomics/dna"
 	"github.com/vertgenlab/gonomics/giraf"
 	"github.com/vertgenlab/gonomics/numbers"
 	"github.com/vertgenlab/gonomics/numbers/parse"
-	"log"
-	"math/rand"
 )
 
 func RandGiraf(graph *GenomeGraph, numReads int, readLen int, randSeed int64) []*giraf.Giraf {
@@ -19,7 +20,8 @@ func RandGiraf(graph *GenomeGraph, numReads int, readLen int, randSeed int64) []
 	if readLen > totalBases { // not a perfect check, but best we can do without a search algorithm
 		log.Fatal("Cannot request more bases than is present in graph")
 	}
-	rand.Seed(randSeed)
+
+	rand.New(rand.NewSource(randSeed))
 
 	for len(answer) < numReads {
 		nodeIdx, pos := RandLocationFast(graph, totalBases)
@@ -101,7 +103,7 @@ func RandSomaticMutations(graph *GenomeGraph, reads []*giraf.Giraf, numSomaticSN
 	var mutationNode, mutationPos []uint32
 	var nodeIdx uint32
 	var pos, readPos uint32
-	rand.Seed(randSeed)
+	rand.New(rand.NewSource(randSeed))
 
 	for i := 0; i < numSomaticSNV; i++ {
 		nodeIdx, pos = RandLocationFast(graph, totalBases)

interval/interval_test.go

@@ -192,15 +192,15 @@ const (
 )
 
 func BenchmarkBuildTree(b *testing.B) {
-	rand.Seed(time.Now().UnixNano())
+	rand.New(rand.NewSource(time.Now().UnixNano()))
 	intervals := generateIntervals(numIntervals, rangeLow, rangeHigh)
 	b.ResetTimer()
 	for n := 0; n < b.N; n++ {
 		BuildTree(intervals)
 	}
 }
 func BenchmarkQueryO(b *testing.B) {
-	rand.Seed(time.Now().UnixNano())
+	rand.New(rand.NewSource(time.Now().UnixNano()))
 	intervals := generateIntervals(numIntervals, rangeLow, rangeHigh)
 	tree := BuildTree(intervals)
 	b.ResetTimer()
@@ -209,7 +209,7 @@ func BenchmarkQueryO(b *testing.B) {
 	}
 }
 func BenchmarkQueryOi(b *testing.B) {
-	rand.Seed(time.Now().UnixNano())
+	rand.New(rand.NewSource(time.Now().UnixNano()))
 	intervals := generateIntervals(numIntervals, rangeLow, rangeHigh)
 	tree := BuildTree(intervals)
 	b.ResetTimer()
@@ -218,7 +218,7 @@ func BenchmarkQueryOi(b *testing.B) {
 	}
 }
 func BenchmarkQueryD(b *testing.B) {
-	rand.Seed(time.Now().UnixNano())
+	rand.New(rand.NewSource(time.Now().UnixNano()))
 	intervals := generateIntervals(numIntervals, rangeLow, rangeHigh)
 	tree := BuildTree(intervals)
 	b.ResetTimer()
@@ -227,7 +227,7 @@ func BenchmarkQueryD(b *testing.B) {
 	}
 }
 func BenchmarkQueryDi(b *testing.B) {
-	rand.Seed(time.Now().UnixNano())
+	rand.New(rand.NewSource(time.Now().UnixNano()))
 	intervals := generateIntervals(numIntervals, rangeLow, rangeHigh)
 	tree := BuildTree(intervals)
 	b.ResetTimer()
@@ -236,7 +236,7 @@ func BenchmarkQueryDi(b *testing.B) {
 	}
 }
 func BenchmarkQueryS(b *testing.B) {
-	rand.Seed(time.Now().UnixNano())
+	rand.New(rand.NewSource(time.Now().UnixNano()))
 	intervals := generateIntervals(numIntervals, rangeLow, rangeHigh)
 	tree := BuildTree(intervals)
 	b.ResetTimer()
@@ -245,7 +245,7 @@ func BenchmarkQueryS(b *testing.B) {
 	}
 }
 func BenchmarkQuerySi(b *testing.B) {
-	rand.Seed(time.Now().UnixNano())
+	rand.New(rand.NewSource(time.Now().UnixNano()))
 	intervals := generateIntervals(numIntervals, rangeLow, rangeHigh)
 	tree := BuildTree(intervals)
 	b.ResetTimer()
@@ -254,7 +254,7 @@ func BenchmarkQuerySi(b *testing.B) {
 	}
 }
 func BenchmarkQueryF(b *testing.B) {
-	rand.Seed(time.Now().UnixNano())
+	rand.New(rand.NewSource(time.Now().UnixNano()))
 	intervals := generateIntervals(numIntervals, rangeLow, rangeHigh)
 	tree := BuildTree(intervals)
 	b.ResetTimer()
@@ -263,7 +263,7 @@ func BenchmarkQueryF(b *testing.B) {
 	}
 }
 func BenchmarkQueryFi(b *testing.B) {
-	rand.Seed(time.Now().UnixNano())
+	rand.New(rand.NewSource(time.Now().UnixNano()))
 	intervals := generateIntervals(numIntervals, rangeLow, rangeHigh)
 	tree := BuildTree(intervals)
 	b.ResetTimer()
@@ -272,7 +272,7 @@ func BenchmarkQueryFi(b *testing.B) {
 	}
 }
 func BenchmarkQueryM(b *testing.B) {
-	rand.Seed(time.Now().UnixNano())
+	rand.New(rand.NewSource(time.Now().UnixNano()))
 	intervals := generateIntervals(numIntervals, rangeLow, rangeHigh)
 	tree := BuildTree(intervals)
 	b.ResetTimer()
@@ -281,7 +281,7 @@ func BenchmarkQueryM(b *testing.B) {
 	}
 }
 func BenchmarkQueryMi(b *testing.B) {
-	rand.Seed(time.Now().UnixNano())
+	rand.New(rand.NewSource(time.Now().UnixNano()))
 	intervals := generateIntervals(numIntervals, rangeLow, rangeHigh)
 	tree := BuildTree(intervals)
 	b.ResetTimer()
@@ -290,7 +290,7 @@ func BenchmarkQueryMi(b *testing.B) {
 	}
 }
 func BenchmarkQueryE(b *testing.B) {
-	rand.Seed(time.Now().UnixNano())
+	rand.New(rand.NewSource(time.Now().UnixNano()))
 	intervals := generateIntervals(numIntervals, rangeLow, rangeHigh)
 	tree := BuildTree(intervals)
 	b.ResetTimer()
@@ -299,7 +299,7 @@ func BenchmarkQueryE(b *testing.B) {
 	}
 }
 func BenchmarkQueryLT(b *testing.B) {
-	rand.Seed(time.Now().UnixNano())
+	rand.New(rand.NewSource(time.Now().UnixNano()))
 	intervals := generateIntervals(numIntervals, rangeLow, rangeHigh)
 	tree := BuildTree(intervals)
 	b.ResetTimer()
@@ -308,7 +308,7 @@ func BenchmarkQueryLT(b *testing.B) {
 	}
 }
 func BenchmarkQueryGT(b *testing.B) {
-	rand.Seed(time.Now().UnixNano())
+	rand.New(rand.NewSource(time.Now().UnixNano()))
 	intervals := generateIntervals(numIntervals, rangeLow, rangeHigh)
 	tree := BuildTree(intervals)
 	b.ResetTimer()
@@ -317,7 +317,7 @@ func BenchmarkQueryGT(b *testing.B) {
 	}
 }
 func BenchmarkQueryAny(b *testing.B) {
-	rand.Seed(time.Now().UnixNano())
+	rand.New(rand.NewSource(time.Now().UnixNano()))
 	intervals := generateIntervals(numIntervals, rangeLow, rangeHigh)
 	tree := BuildTree(intervals)
 	b.ResetTimer()
@@ -326,7 +326,7 @@ func BenchmarkQueryAny(b *testing.B) {
 	}
 }
 func BenchmarkQueryWithin(b *testing.B) {
-	rand.Seed(time.Now().UnixNano())
+	rand.New(rand.NewSource(time.Now().UnixNano()))
 	intervals := generateIntervals(numIntervals, rangeLow, rangeHigh)
 	tree := BuildTree(intervals)
 	b.ResetTimer()
@@ -335,7 +335,7 @@ func BenchmarkQueryWithin(b *testing.B) {
 	}
 }
 func BenchmarkQueryStart(b *testing.B) {
-	rand.Seed(time.Now().UnixNano())
+	rand.New(rand.NewSource(time.Now().UnixNano()))
 	intervals := generateIntervals(numIntervals, rangeLow, rangeHigh)
 	tree := BuildTree(intervals)
 	b.ResetTimer()
@@ -344,7 +344,7 @@ func BenchmarkQueryStart(b *testing.B) {
 	}
 }
 func BenchmarkQueryEnd(b *testing.B) {
-	rand.Seed(time.Now().UnixNano())
+	rand.New(rand.NewSource(time.Now().UnixNano()))
 	intervals := generateIntervals(numIntervals, rangeLow, rangeHigh)
 	tree := BuildTree(intervals)
 	b.ResetTimer()