Add method to stats.Map to output JSON - close #16

cmd/bamstats/bamstats.go

@@ -5,6 +5,7 @@ import (
 
 	log "github.com/Sirupsen/logrus"
 	"github.com/guigolab/bamstats"
+	"github.com/guigolab/bamstats/utils"
 	"github.com/spf13/cobra"
 )
 
@@ -33,7 +34,9 @@ func run(cmd *cobra.Command, args []string) (err error) {
 	if err != nil {
 		return
 	}
-	bamstats.WriteOutput(output, allStats)
+
+	w := utils.NewWriter(output)
+	allStats.OutputJSON(w)
 
 	return
 }

process.go

@@ -12,7 +12,6 @@ import (
 	"github.com/guigolab/bamstats/config"
 	"github.com/guigolab/bamstats/sam"
 	"github.com/guigolab/bamstats/stats"
-	"github.com/guigolab/bamstats/utils"
 )
 
 func init() {
@@ -134,11 +133,6 @@ func Process(bamFile string, anno string, cpu int, maxBuf int, reads int, uniq b
 	return allStats, nil
 }
 
-func WriteOutput(output string, st stats.Map) {
-	out := utils.NewOutput(output)
-	utils.OutputJSON(out, st)
-}
-
 func makeStatsMap(index *annotation.RtreeMap, cfg *config.Config) stats.Map {
 	m := make(stats.Map)
 	m.Add("general", stats.NewGeneralStats())

stats/stats.go

@@ -1,8 +1,10 @@
 package stats
 
 import (
+	"bufio"
 	"encoding/json"
 	"fmt"
+	"io"
 	"strconv"
 
 	"github.com/guigolab/bamstats/sam"
@@ -49,6 +51,19 @@ func (sm Map) Add(key string, s Stats) {
 	sm[key] = s
 }
 
+// OutputJSON writes sm to the wrtier as JSON
+func (sm Map) OutputJSON(writer io.Writer) error {
+	b, err := json.MarshalIndent(sm, "", "\t")
+	if err != nil {
+		return err
+	}
+	writer.Write(b)
+	if w, ok := writer.(*bufio.Writer); ok {
+		w.Flush()
+	}
+	return nil
+}
+
 // NewMap creates and instance of a stats.Map
 // func NewMap(general, coverage, uniq bool) Map {
 // 	m := make(Map)

utils/utils.go

@@ -22,24 +22,16 @@ func Min(a, b int) int {
 	return b
 }
 
-// OutputJSON writes the json representation of stats to an io.Writer
-func OutputJSON(writer io.Writer, stats interface{}) {
-	b, err := json.MarshalIndent(stats, "", "\t")
-	Check(err)
-	writer.Write(b)
-	if w, ok := writer.(*bufio.Writer); ok {
-		w.Flush()
-	}
-}
-
-// NewOutput return a new io.Writer given an output file name. If the file name is '-' os.Stdout is returned.
-func NewOutput(output string) io.Writer {
+// NewWriter return a new io.Writer given an output file name. If the file name is '-' os.Stdout is returned.
+func NewWriter(output string) io.Writer {
 	switch output {
 	case "-":
 		return os.Stdout
 	default:
 		f, err := os.Create(output)
-		Check(err)
+		if err != nil {
+			return nil
+		}
 		return bufio.NewWriter(f)
 	}
 }