fix calling rand.New

Author: shenwei356

seqkit/cmd/sample.go

@@ -93,7 +93,7 @@ Attention:
 		checkError(err)
 		defer outfh.Close()
 
-		rand.Seed(seed)
+		_rand := rand.New(rand.NewSource(seed))
 		// randg := randomFloat64Generator(seed)
 
 		n := int64(0)
@@ -139,7 +139,7 @@ Attention:
 					}
 
 					// if <-randg <= proportion {
-					if rand.Float64() <= proportion {
+					if _rand.Float64() <= proportion {
 						n++
 						record.FormatToWriter(outfh, config.LineWidth)
 						if n == number {
@@ -163,7 +163,7 @@ Attention:
 
 				for _, record := range records {
 					// if <-randg <= proportion {
-					if rand.Float64() <= proportion {
+					if _rand.Float64() <= proportion {
 						n++
 						record.FormatToWriter(outfh, config.LineWidth)
 						if n == number {
@@ -194,7 +194,7 @@ Attention:
 				}
 
 				// if <-randg <= proportion {
-				if rand.Float64() <= proportion {
+				if _rand.Float64() <= proportion {
 					n++
 					record.FormatToWriter(outfh, config.LineWidth)
 				}

seqkit/cmd/shuffle.go

@@ -30,7 +30,6 @@ import (
 	"github.com/shenwei356/bio/seq"
 	"github.com/shenwei356/bio/seqio/fai"
 	"github.com/shenwei356/bio/seqio/fastx"
-	"github.com/shenwei356/util/randutil"
 	"github.com/shenwei356/xopen"
 	"github.com/spf13/cobra"
 )
@@ -128,12 +127,14 @@ Attention:
 				log.Infof("%d sequences loaded", len(sequences))
 				log.Infof("shuffle ...")
 			}
-			rand.Seed(seed)
 			indices := make([]int, len(index2name))
 			for i := 0; i < len(index2name); i++ {
 				indices[i] = i
 			}
-			randutil.Shuffle(indices)
+
+			rand.New(rand.NewSource(seed)).Shuffle(len(indices), func(i, j int) {
+				indices[i], indices[j] = indices[j], indices[i]
+			})
 
 			if !quiet {
 				log.Infof("output ...")
@@ -219,12 +220,14 @@ Attention:
 		if !quiet {
 			log.Infof("shuffle ...")
 		}
-		rand.Seed(seed)
 		indices := make([]int, len(index2name))
 		for i := 0; i < len(index2name); i++ {
 			indices[i] = i
 		}
-		randutil.Shuffle(indices)
+
+		rand.New(rand.NewSource(seed)).Shuffle(len(indices), func(i, j int) {
+			indices[i], indices[j] = indices[j], indices[i]
+		})
 
 		if !quiet {
 			log.Infof("output ...")

seqkit/cmd/util.go

@@ -24,7 +24,6 @@ import (
 	"bytes"
 	"fmt"
 	"io"
-	"math/rand"
 	"os"
 	"os/exec"
 	"regexp"
@@ -492,18 +491,6 @@ func checkFileFormat(format string) {
 	}
 }
 
-// it's slow, do not use
-func randomFloat64Generator(seed int64) chan float64 {
-	rand.Seed(seed)
-	ch := make(chan float64, 1024)
-	go func() {
-		for {
-			ch <- rand.Float64()
-		}
-	}()
-	return ch
-}
-
 func wrapByteSlice(s []byte, width int, buffer *bytes.Buffer) ([]byte, *bytes.Buffer) {
 	if width < 1 {
 		return s, buffer

tests/test.sh

@@ -332,7 +332,7 @@ rm t.*
 file=tests/hairpin.fa
 
 testseq() {
-    cat $file | $app head -n 100 | $app rmdup
+    cat $file | $app head -n 100 | $app rmdup --quiet
 }
 fun() {
     testseq | $app split -i -f