Propagate genome arg.

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

diff --git a/vcf2fasta.go b/vcf2fasta.go
index 6083e4c04130b00a1fe2b3df82f1da4994466d37..d6cc9bba1cd83baddf12d0b2173e1b8c67a89c82 100644 (file)
--- a/vcf2fasta.go
+++ b/vcf2fasta.go
@@ -112,7 +112,7 @@ func (cmd *vcf2fasta) RunCommand(prog string, args []string, stdin io.Reader, st
                                },
                        },
                }
-               err = runner.TranslatePaths(&cmd.refFile)
+               err = runner.TranslatePaths(&cmd.refFile, &cmd.genomeFile)
                if err != nil {
                        return 1
                }
@@ -123,7 +123,12 @@ func (cmd *vcf2fasta) RunCommand(prog string, args []string, stdin io.Reader, st
                                return 1
                        }
                }
-               runner.Args = append([]string{"vcf2fasta", "-local=true", "-ref", cmd.refFile, fmt.Sprintf("-mask=%v", cmd.mask), "-gvcf-regions.py", "/gvcf_regions.py", "-output-dir", "/mnt/output"}, inputs...)
+               runner.Args = append([]string{"vcf2fasta",
+                       "-local=true",
+                       "-ref", cmd.refFile, fmt.Sprintf("-mask=%v", cmd.mask),
+                       "-genome", cmd.genomeFile,
+                       "-gvcf-regions.py", "/gvcf_regions.py",
+                       "-output-dir", "/mnt/output"}, inputs...)
                var output string
                output, err = runner.Run()
                if err != nil {