Kill other children and exit early if one child process fails.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

diff --git a/vcf2fasta.go b/vcf2fasta.go
index 1e7e2769266d616705618bc5f5bae828c245abe5..afafdd70a45c99f2102ce736e350bae8550658f3 100644 (file)
--- a/vcf2fasta.go
+++ b/vcf2fasta.go
@@ -4,6 +4,7 @@ import (
        "bufio"
        "bytes"
        "compress/gzip"
+       "context"
        "errors"
        "flag"
        "fmt"
@@ -206,6 +207,9 @@ func maybeInDocker(args, mountfiles []string) []string {
 }
 
 func (cmd *vcf2fasta) vcf2fasta(infile string, phase int) error {
+       ctx, cancel := context.WithCancel(context.Background())
+       defer cancel()
+
        _, basename := filepath.Split(infile)
        outfile := filepath.Join(cmd.outputDir, fmt.Sprintf("%s.%d.fasta.gz", basename, phase))
        outf, err := os.OpenFile(outfile, os.O_CREATE|os.O_WRONLY, 0777)
@@ -228,7 +232,7 @@ func (cmd *vcf2fasta) vcf2fasta(infile string, phase int) error {
 
                var regions bytes.Buffer
                bedargs := []string{"python2", "-", "--gvcf_type", "gatk", infile}
-               bed := exec.Command(bedargs[0], bedargs[1:]...)
+               bed := exec.CommandContext(ctx, bedargs[0], bedargs[1:]...)
                bed.Stdin = bytes.NewBuffer(cmd.gvcfRegionsPyData)
                bed.Stdout = &regions
                bed.Stderr = cmd.stderr
@@ -313,7 +317,7 @@ func (cmd *vcf2fasta) vcf2fasta(infile string, phase int) error {
 
                        bedcompargs := []string{"bedtools", "complement", "-i", regionsFile, "-g", "/dev/stdin"}
                        bedcompargs = maybeInDocker(bedcompargs, []string{cmd.genomeFile})
-                       bedcomp := exec.Command(bedcompargs[0], bedcompargs[1:]...)
+                       bedcomp := exec.CommandContext(ctx, bedcompargs[0], bedcompargs[1:]...)
                        bedcomp.Stdin = &sortedGenomeFile
                        bedcomp.Stdout = maskfifow
                        bedcomp.Stderr = cmd.stderr
@@ -350,7 +354,7 @@ func (cmd *vcf2fasta) vcf2fasta(infile string, phase int) error {
                }
                consargs = maybeInDocker(consargs, mounts)
 
-               consensus := exec.Command(consargs[0], consargs[1:]...)
+               consensus := exec.CommandContext(ctx, consargs[0], consargs[1:]...)
                consensus.Stderr = os.Stderr
                consensus.Stdout = gzipw
                consensus.Stderr = cmd.stderr
@@ -375,6 +379,7 @@ func (cmd *vcf2fasta) vcf2fasta(infile string, phase int) error {
 
        for err := range errs {
                if err != nil {
+                       cancel()
                        wg.Wait()
                        return err
                }