Don't pass -gvcf-type="" to gvcf_regions.py.

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

diff --git a/vcf2fasta.go b/vcf2fasta.go
index 7f8df2b5ae4850ffc6a9ff78a88ea67d81c04adb..f3faccf4f2b4738e756e6545b2a99dd564878112 100644 (file)
--- a/vcf2fasta.go
+++ b/vcf2fasta.go
@@ -282,8 +282,13 @@ func (cmd *vcf2fasta) vcf2fasta(infile string, phase int) error {
                if err = scanner.Err(); err != nil {
                        return fmt.Errorf("error scanning input file %q: %s", infile, err)
                }
+
                var regions bytes.Buffer
-               bedargs := []string{"python2", "-", "--gvcf_type", cmd.gvcfType, infile}
+               bedargs := []string{"python2", "-"}
+               if cmd.gvcfType != "" {
+                       bedargs = append(bedargs, "--gvcf_type", cmd.gvcfType)
+               }
+               bedargs = append(bedargs, infile)
                bed := exec.CommandContext(ctx, bedargs[0], bedargs[1:]...)
                bed.Stdin = bytes.NewBuffer(cmd.gvcfRegionsPyData)
                bed.Stdout = &regions