From 41aeefd16884250c54cee3fc91a7927c6167f6f1 Mon Sep 17 00:00:00 2001
From: Tom Clegg <tom@tomclegg.ca>
Date: Tue, 10 Mar 2020 17:11:17 -0400
Subject: [PATCH] Fix docker mounts.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
---
 vcf2fasta.go | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vcf2fasta.go b/vcf2fasta.go
index 6c8ec5fbcc..383ef85ca7 100644
--- a/vcf2fasta.go
+++ b/vcf2fasta.go
@@ -238,7 +238,7 @@ func (cmd *vcf2fasta) vcf2fasta(infile string, phase int) error {
 			return err
 		}
 		bedcompargs := []string{"bedtools", "complement", "-i", "/dev/stdin", "-g", cmd.genomeFile}
-		bedcompargs = maybeInDocker(bedcompargs, []string{cmd.refFile, infile})
+		bedcompargs = maybeInDocker(bedcompargs, []string{cmd.genomeFile})
 		bedcomp := exec.Command(bedcompargs[0], bedcompargs[1:]...)
 		bedcomp.Stdin = bedr
 		bedcomp.Stdout = bedcompw
-- 
2.30.2