Working with mosdepth

Author: dschles

.gitignore

@@ -1,3 +1,4 @@
 *.json
 *.json.gz
 coverage
+pkged.go 

go.mod

@@ -8,6 +8,7 @@ require (
 	github.com/brentp/irelate v0.0.1
 	github.com/brentp/vcfgo v0.0.0-20190824021612-654ed2e5945d // indirect
 	github.com/json-iterator/go v1.1.11
-	github.com/markbates/pkger v0.17.1
 	github.com/pkg/errors v0.9.1 // indirect
+	github.com/stretchr/testify v1.4.0 // indirect
+	gopkg.in/yaml.v2 v2.2.7 // indirect
 )

go.sum

@@ -14,20 +14,15 @@ github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSs
 github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c=
 github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
 github.com/go-gl/glfw/v3.3/glfw v0.0.0-20191125211704-12ad95a8df72/go.mod h1:tQ2UAYgL5IevRw8kRxooKSPJfGvJ9fJQFa0TUsXzTg8=
-github.com/gobuffalo/here v0.6.0 h1:hYrd0a6gDmWxBM4TnrGw8mQg24iSVoIkHEk7FodQcBI=
-github.com/gobuffalo/here v0.6.0/go.mod h1:wAG085dHOYqUpf+Ap+WOdrPTp5IYcDAs/x7PLa8Y5fM=
 github.com/google/gofuzz v1.0.0/go.mod h1:dBl0BpW6vV/+mYPU4Po3pmUjxk6FQPldtuIdl/M65Eg=
 github.com/json-iterator/go v1.1.11 h1:uVUAXhF2To8cbw/3xN3pxj6kk7TYKs98NIrTqPlMWAQ=
 github.com/json-iterator/go v1.1.11/go.mod h1:KdQUCv79m/52Kvf8AW2vK1V8akMuk1QjK/uOdHXbAo4=
 github.com/kortschak/utter v0.0.0-20190412033250-50fe362e6560/go.mod h1:oDr41C7kH9wvAikWyFhr6UFr8R7nelpmCF5XR5rL7I8=
-github.com/kr/pretty v0.1.0/go.mod h1:dAy3ld7l9f0ibDNOQOHHMYYIIbhfbHSm3C4ZsoJORNo=
 github.com/kr/pretty v0.2.0 h1:s5hAObm+yFO5uHYt5dYjxi2rXrsnmRpJx4OYvIWUaQs=
 github.com/kr/pretty v0.2.0/go.mod h1:ipq/a2n7PKx3OHsz4KJII5eveXtPO4qwEXGdVfWzfnI=
 github.com/kr/pty v1.1.1/go.mod h1:pFQYn66WHrOpPYNljwOMqo10TkYh1fy3cYio2l3bCsQ=
 github.com/kr/text v0.1.0 h1:45sCR5RtlFHMR4UwH9sdQ5TC8v0qDQCHnXt+kaKSTVE=
 github.com/kr/text v0.1.0/go.mod h1:4Jbv+DJW3UT/LiOwJeYQe1efqtUx/iVham/4vfdArNI=
-github.com/markbates/pkger v0.17.1 h1:/MKEtWqtc0mZvu9OinB9UzVN9iYCwLWuyUv4Bw+PCno=
-github.com/markbates/pkger v0.17.1/go.mod h1:0JoVlrol20BSywW79rN3kdFFsE5xYM+rSCQDXbLhiuI=
 github.com/modern-go/concurrent v0.0.0-20180228061459-e0a39a4cb421 h1:ZqeYNhU3OHLH3mGKHDcjJRFFRrJa6eAM5H+CtDdOsPc=
 github.com/modern-go/concurrent v0.0.0-20180228061459-e0a39a4cb421/go.mod h1:6dJC0mAP4ikYIbvyc7fijjWJddQyLn8Ig3JB5CqoB9Q=
 github.com/modern-go/reflect2 v0.0.0-20180701023420-4b7aa43c6742 h1:Esafd1046DLDQ0W1YjYsBW+p8U2u7vzgW2SQVmlNazg=
@@ -59,7 +54,6 @@ golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ=
 golang.org/x/tools v0.0.0-20191012152004-8de300cfc20a/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo=
 golang.org/x/xerrors v0.0.0-20190717185122-a985d3407aa7/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0=
 gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
-gopkg.in/check.v1 v1.0.0-20180628173108-788fd7840127/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
 gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15 h1:YR8cESwS4TdDjEe65xsg0ogRM/Nc3DYOhEAlW+xobZo=
 gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
 gopkg.in/yaml.v2 v2.2.2/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI=

main.go

@@ -3,9 +3,13 @@ package main
 import (
 	"flag"
 	"log"
+	"os"
+	"time"
 )
 
 func main() {
+	t0 := time.Now()
+
 	// Coverage vcf
 	vcf := flag.String("vcf", "", "VCF file with coverage (GATK-format).")
 	bed := flag.String("bed", "", "BED file with coverage (Mosdepth-format).")
@@ -25,6 +29,8 @@ func main() {
 	case *bed != "":
 		// Intersect coverage with transcripts
 		getMosdepth(*bed)
+		log.Printf("Executed in %.2f seconds\n", time.Since(t0).Seconds())
+		os.Exit(0)
 	}
 
 	// Output coverage to JSON file

mosdepth.go

@@ -2,16 +2,14 @@ package main
 
 import (
 	"compress/gzip"
+	_ "embed"
 	"encoding/csv"
 	"fmt"
 	"io"
-	"io/ioutil"
 	"log"
 	"os"
 	"strconv"
 	"strings"
-
-	"github.com/markbates/pkger"
 )
 
 type Gene struct {
@@ -32,20 +30,12 @@ type Bed struct {
 	x30   int
 }
 
+//go:embed genes.bed
+var genesFile string
+
 func getMosdepth(coverageBed string) {
 	targets := parseMosdepthBed(coverageBed)
 
-	f, err := pkger.Open("genes.bed")
-	if err != nil {
-		log.Fatalln("couldn't find genes.bed")
-	}
-	defer f.Close()
-
-	genesFile, err := ioutil.ReadAll(f)
-	if err != nil {
-		log.Fatal("unable to open genes file")
-	}
-
 	geneLines := strings.Split(string(genesFile), "\n")
 
 	for _, line := range geneLines {
@@ -85,7 +75,7 @@ func getMosdepth(coverageBed string) {
 			}
 		}
 
-		fmt.Printf("%s\t%s\tCount: %d\tTotal Bases: %d\tCoverage 5x: %d\t10x: %d\t20x: %d\t30x: %d", gene.ensg, gene.symbol, overlapCount, totalTargets, totalCovered5x, totalCovered10x, totalCovered20x, totalCovered30x)
+		fmt.Printf("%s\t%s\tCount: %d\tTotal Bases: %d\tCoverage 5x: %d\t10x: %d\t20x: %d\t30x: %d\n", gene.ensg, gene.symbol, overlapCount, totalTargets, totalCovered5x, totalCovered10x, totalCovered20x, totalCovered30x)
 	}
 }