Don't try to pass fd 3 to docker.

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

diff --git a/vcf2fasta.go b/vcf2fasta.go
index f7515c40f7d4b43052549533232e3749ecf423e1..9263b9358d8cf24fe3606c3f5a2a6c97c8522411 100644 (file)
--- a/vcf2fasta.go
+++ b/vcf2fasta.go
@@ -247,7 +247,7 @@ func (cmd *vcf2fasta) vcf2fasta(infile string, phase int) error {
                defer wg.Done()
                consargs := []string{"bcftools", "consensus", "--fasta-ref", cmd.refFile, "-H", fmt.Sprint(phase)}
                if maskfile != nil {
-                       consargs = append(consargs, "--mask", "/dev/fd/3")
+                       consargs = append(consargs, "--mask", "/dev/stdin")
                }
                consargs = append(consargs, infile)
                indexsuffix := ".tbi"
@@ -260,7 +260,7 @@ func (cmd *vcf2fasta) vcf2fasta(infile string, phase int) error {
                consensus.Stderr = os.Stderr
                consensus.Stdout = gzipw
                if maskfile != nil {
-                       consensus.ExtraFiles = []*os.File{maskfile}
+                       consensus.Stdin = maskfile
                }
                log.Printf("running %v", consensus.Args)
                err = consensus.Run()