update output prefix

README.md

@@ -9,7 +9,7 @@ Simple peak caller for CUT&TAG data
 Download the latest release binary specific for your operating system:
 
 ```
-wget -O gopeaks https://github.com/maxsonBraunLab/gopeaks/releases/download/v0.1.7/gopeaks-linux-amd64
+wget -O gopeaks https://github.com/maxsonBraunLab/gopeaks/releases/download/v0.1.9/gopeaks-linux-amd64
 chmod +x gopeaks
 ```
 
@@ -19,30 +19,57 @@ chmod +x gopeaks
 ./gopeaks -h 
 Usage of ./gopeaks:
   -bam string
-        Bam file with
+    	Bam file with
   -control string
-        Bam file with contriol signal to be subtracted
+    	Bam file with contriol signal to be subtracted
   -cs string
-        Supply chromosome sizes for the alignment genome if not found in the bam header
+    	Supply chromosome sizes for the alignment genome if not found in the bam header
   -mdist int
-        Merge distance for nearby peaks (default 150)
+    	Merge distance for nearby peaks (default 150)
   -minwidth int
-        Minimum width to be considered a peak (default 150)
+    	Minimum width to be considered a peak (default 150)
   -mr int
-        Min reads per coverage bin to be considered (default 15)
-  -of string
-        Output file to write peaks to (default "peaks.bed")
+    	Min reads per coverage bin to be considered (default 15)
+  -o string
+    	Output prefiex to write peaks and metrics file (default "sample")
   -pval float
-        Pvalue threshold for keeping a peak bin (default 0.05)
+    	Pvalue threshold for keeping a peak bin (default 0.05)
   -slide int
-        Slide size for coverage bins (default 50)
+    	Slide size for coverage bins (default 50)
   -step int
-        Bin size for coverage bins (default 100)
+    	Bin size for coverage bins (default 100)
+  -version
+    	Print the current gopeaks version
 ```
 
 
 ## call peaks on a bam file using an IgG control
 
 ```
-./gopeaks -bam ../chr1.bam -control chr1_igg.bam -cs data/hg38.known.chrom.sizes -of chr1.bed
+./gopeaks -bam ../chr1.bam -control chr1_igg.bam -cs data/hg38.known.chrom.sizes -o chr1
+```
+
+## Output
+
+Two output files are generated each with the output prefix ${prefix}, set to "sample" by default.
+
+    - sample_peaks.bed
+    - sample_gopeaks.json
+
+```
+head sample_peaks.bed
+chr1	9950	10550
+chr1	21250	22650
+chr1	96050	97050
+```
+
+```
+cat sample_gopeaks.json
+{
+	"gopeaks_version": "0.1.9",
+	"date": "2021-08-06 11:4:58 AM",
+	"elapsed": "1m23.43085221s",
+	"prefix": "sample",
+	"peak_counts": 4765
+}
 ```

conda/meta.yaml

@@ -6,7 +6,6 @@ package:
 
 source:
    - url: https://github.com/maxsonBraunLab/gopeaks/archive/refs/tags/v{{ version }}.tar.gz
-     sha256: 85d98aea13617a211e82465629427904e42635973fd23540a309601ce15955da
 
 build:
   number: 0

gopeaks.go

@@ -14,24 +14,24 @@ import (
 	"gonum.org/v1/gonum/stat/distuv"
 )
 
-const gopeaks_version = "0.1.8"
+const gopeaks_version = "0.1.9"
 
 type Metrics struct {
 	Version string `json:"gopeaks_version"`
 	Date    string `json:"date"`
 	Elapsed string `json:"elapsed"`
-	Outfile string `json:"outfile"`
+	Prefix  string `json:"prefix"`
 	Peaks   int    `json:"peak_counts"`
 }
 
-func (m *Metrics) Log() {
+func (m *Metrics) Log(op string) {
 	resp, err := json.MarshalIndent(m, "", "\t")
 	if err != nil {
 		fmt.Println(err)
 		os.Exit(1)
 	}
 
-	f, err := os.Create("gopeaks-metrics.json")
+	f, err := os.Create(op + "_gopeaks.json")
 	defer f.Close()
 	if err != nil {
 		fmt.Println(err)
@@ -51,7 +51,7 @@ func main() {
 	bam := flag.String("bam", "", "Bam file with ")
 	cs := flag.String("cs", "", "Supply chromosome sizes for the alignment genome if not found in the bam header")
 	within := flag.Int("mdist", 150, "Merge distance for nearby peaks")
-	outfile := flag.String("of", "peaks.bed", "Output file to write peaks to")
+	outprefix := flag.String("o", "sample", "Output prefiex to write peaks and metrics file")
 	minreads := flag.Int("mr", 15, "Min reads per coverage bin to be considered")
 	pval := flag.Float64("pval", 0.05, "Pvalue threshold for keeping a peak bin")
 	step := flag.Int("step", 100, "Bin size for coverage bins")
@@ -122,7 +122,8 @@ func main() {
 	// callpeaks
 	peaks := callpeaks(binCounts, float64(nreads), *within, *minwidth, *minreads, *pval)
 
-	err = peaks.ExportBed3(*outfile, false)
+	outfile := *outprefix + "_peaks.bed"
+	err = peaks.ExportBed3(outfile, false)
 	if err != nil {
 		logrus.Errorln(err)
 	}
@@ -132,12 +133,12 @@ func main() {
 		Version: gopeaks_version,
 		Date:    time.Now().Format("2006-01-02 3:4:5 PM"),
 		Elapsed: time.Since(startTime).String(),
-		Outfile: *outfile,
+		Prefix:  *outprefix,
 		Peaks:   peaks.Length(),
 	}
 
 	// log metrics to file
-	metrics.Log()
+	metrics.Log(*outprefix)
 }
 
 func scaleTreatToControl(counts []float64, s1 []float64, s2 []float64) []float64 {