better output for bits presentation of encoded k-mers

CHANGES.md

@@ -1,3 +1,5 @@
+- v0.6.2
+    - `unikmer encode`: better output for bits presentation of encoded k-mers (`-a/--all`)
 - v0.6.1
     - `unikmer dump`: 
         - new option `-K/--canonical` to keep the canonical k-mers.

kmer.go

@@ -223,6 +223,9 @@ func RevComp(code uint64, k int) (c uint64) {
 // bit2base is for mapping bit to base.
 var bit2base = [4]byte{'A', 'C', 'G', 'T'}
 
+// bit2str is for output bits string
+var bit2str = [4]string{"00", "01", "10", "11"}
+
 // Decode converts the code to original seq
 func Decode(code uint64, k int) []byte {
 	if k <= 0 || k > 32 {
@@ -311,3 +314,12 @@ func (kcode KmerCode) Bytes() []byte {
 func (kcode KmerCode) String() string {
 	return string(Decode(kcode.Code, kcode.K))
 }
+
+// BitsString returns code to string
+func (kcode KmerCode) BitsString() string {
+	var buf bytes.Buffer
+	for _, b := range Decode(kcode.Code, kcode.K) {
+		buf.WriteString(bit2str[base2bit[b]])
+	}
+	return buf.String()
+}

unikmer/cmd/encode.go

@@ -103,7 +103,7 @@ var encodeCmd = &cobra.Command{
 					}
 
 					if all {
-						outfh.WriteString(fmt.Sprintf("%s\t%s\t%d\t%b\n", line, kcode.String(), kcode.Code, kcode.Code))
+						outfh.WriteString(fmt.Sprintf("%s\t%s\t%d\t%s\n", line, kcode.String(), kcode.Code, kcode.BitsString()))
 					} else {
 						outfh.WriteString(fmt.Sprintf("%d\n", kcode.Code))
 					}

unikmer/cmd/version.go

@@ -29,7 +29,7 @@ import (
 )
 
 // VERSION is the version
-var VERSION = "0.6.1"
+var VERSION = "0.6.2"
 
 // versionCmd represents the version command
 var versionCmd = &cobra.Command{