vcf2fasta -mask cont'd.

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

diff --git a/vcf2fasta.go b/vcf2fasta.go
index 00e62f549e43acd3c092736487de0eb71e2dc324..f7515c40f7d4b43052549533232e3749ecf423e1 100644 (file)
--- a/vcf2fasta.go
+++ b/vcf2fasta.go
@@ -220,6 +220,7 @@ func (cmd *vcf2fasta) vcf2fasta(infile string, phase int) error {
                wg.Add(1)
                go func() {
                        defer wg.Done()
+                       log.Printf("running %v", bed.Args)
                        errs <- bed.Run()
                }()
 
@@ -235,43 +236,55 @@ func (cmd *vcf2fasta) vcf2fasta(infile string, phase int) error {
                wg.Add(1)
                go func() {
                        defer wg.Done()
+                       log.Printf("running %v", bedcomp.Args)
                        errs <- bedcomp.Run()
                }()
                maskfile = bedcompr
        }
 
-       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, infile)
-       indexsuffix := ".tbi"
-       if _, err := os.Stat(infile + ".csi"); err == nil {
-               indexsuffix = ".csi"
-       }
-       consargs = maybeInDocker(consargs, []string{infile, infile + indexsuffix, cmd.refFile})
+       wg.Add(1)
+       go func() {
+               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, infile)
+               indexsuffix := ".tbi"
+               if _, err := os.Stat(infile + ".csi"); err == nil {
+                       indexsuffix = ".csi"
+               }
+               consargs = maybeInDocker(consargs, []string{infile, infile + indexsuffix, cmd.refFile})
 
-       consensus := exec.Command(consargs[0], consargs[1:]...)
-       consensus.Stderr = os.Stderr
-       consensus.Stdout = gzipw
-       if maskfile != nil {
-               consensus.ExtraFiles = []*os.File{maskfile}
-       }
-       err = consensus.Start()
-       if err != nil {
-               return err
-       }
-       err = consensus.Wait()
-       if err != nil {
-               return err
-       }
-       err = gzipw.Close()
-       if err != nil {
-               return err
-       }
-       err = outf.Close()
-       if err != nil {
-               return err
+               consensus := exec.Command(consargs[0], consargs[1:]...)
+               consensus.Stderr = os.Stderr
+               consensus.Stdout = gzipw
+               if maskfile != nil {
+                       consensus.ExtraFiles = []*os.File{maskfile}
+               }
+               log.Printf("running %v", consensus.Args)
+               err = consensus.Run()
+               if err != nil {
+                       errs <- err
+                       return
+               }
+               err = gzipw.Close()
+               if err != nil {
+                       errs <- err
+                       return
+               }
+               errs <- outf.Close()
+       }()
+
+       go func() {
+               wg.Wait()
+               close(errs)
+       }()
+
+       for err := range errs {
+               if err != nil {
+                       return err
+               }
        }
        return nil
 }