Show stderr from children.

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

diff --git a/vcf2fasta.go b/vcf2fasta.go
index 9263b9358d8cf24fe3606c3f5a2a6c97c8522411..0e93e55407ec8e293e90f07943e26513ecb361dc 100644 (file)
--- a/vcf2fasta.go
+++ b/vcf2fasta.go
@@ -30,6 +30,8 @@ type vcf2fasta struct {
        outputDir         string
        runLocal          bool
        vcpus             int
+
+       stderr io.Writer
 }
 
 func (cmd *vcf2fasta) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
@@ -63,6 +65,7 @@ func (cmd *vcf2fasta) RunCommand(prog string, args []string, stdin io.Reader, st
                flags.Usage()
                return 2
        }
+       cmd.stderr = stderr
 
        if *pprof != "" {
                go func() {
@@ -217,6 +220,7 @@ func (cmd *vcf2fasta) vcf2fasta(infile string, phase int) error {
                bed := exec.Command(bedargs[0], bedargs[1:]...)
                bed.Stdin = bytes.NewBuffer(cmd.gvcfRegionsPyData)
                bed.Stdout = bedw
+               bed.Stderr = cmd.stderr
                wg.Add(1)
                go func() {
                        defer wg.Done()
@@ -233,6 +237,7 @@ func (cmd *vcf2fasta) vcf2fasta(infile string, phase int) error {
                bedcomp := exec.Command(bedcompargs[0], bedcompargs[1:]...)
                bedcomp.Stdin = bedr
                bedcomp.Stdout = bedcompw
+               bedcomp.Stderr = cmd.stderr
                wg.Add(1)
                go func() {
                        defer wg.Done()
@@ -259,6 +264,7 @@ func (cmd *vcf2fasta) vcf2fasta(infile string, phase int) error {
                consensus := exec.Command(consargs[0], consargs[1:]...)
                consensus.Stderr = os.Stderr
                consensus.Stdout = gzipw
+               consensus.Stderr = cmd.stderr
                if maskfile != nil {
                        consensus.Stdin = maskfile
                }