Connect stdin/stdout in docker containers.

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

diff --git a/vcf2fasta.go b/vcf2fasta.go
index 7b198d4f71ec11fa648ffa1cef35c657b5d4001c..e02f77556c66f39033074ff5c5bbdb6ab0ecc7c7 100644 (file)
--- a/vcf2fasta.go
+++ b/vcf2fasta.go
@@ -187,7 +187,7 @@ func maybeInDocker(args, mountfiles []string) []string {
                return args
        }
        dockerrun := []string{
-               "docker", "run", "--rm",
+               "docker", "run", "--rm", "-i",
                "--log-driver=none",
        }
        for _, f := range mountfiles {
@@ -229,6 +229,7 @@ func (cmd *vcf2fasta) vcf2fasta(infile string, phase int) error {
                wg.Add(1)
                go func() {
                        defer wg.Done()
+                       defer bedw.Close()
                        log.Printf("running %v", bed.Args)
                        err := bed.Run()
                        if err != nil {
@@ -249,6 +250,7 @@ func (cmd *vcf2fasta) vcf2fasta(infile string, phase int) error {
                wg.Add(1)
                go func() {
                        defer wg.Done()
+                       defer bedcompw.Close()
                        log.Printf("running %v", bedcomp.Args)
                        err := bedcomp.Run()
                        if err != nil {