Don't pipe gvcf_regions to bedtools. Avoid short-read race bug.

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

diff --git a/vcf2fasta.go b/vcf2fasta.go
index 04e0b7422f3970eaf1271311226a8a3c6a4a6ae4..6083e4c04130b00a1fe2b3df82f1da4994466d37 100644 (file)
--- a/vcf2fasta.go
+++ b/vcf2fasta.go
@@ -213,31 +213,23 @@ func (cmd *vcf2fasta) vcf2fasta(infile string, phase int) error {
        var maskfifo string // filename of mask fifo if we're running bedtools, otherwise ""
 
        var wg sync.WaitGroup
-       errs := make(chan error, 3)
+       errs := make(chan error, 2)
        if cmd.mask {
                if cmd.genomeFile == "" {
                        return errors.New("cannot apply mask without -genome argument")
                }
-               bedr, bedw, err := os.Pipe()
-               if err != nil {
-                       return err
-               }
+               var regions bytes.Buffer
                bedargs := []string{"python", "-", "--gvcf_type", "gatk", infile}
                bed := exec.Command(bedargs[0], bedargs[1:]...)
                bed.Stdin = bytes.NewBuffer(cmd.gvcfRegionsPyData)
-               bed.Stdout = bedw
+               bed.Stdout = &regions
                bed.Stderr = cmd.stderr
-               wg.Add(1)
-               go func() {
-                       defer wg.Done()
-                       defer bedw.Close()
-                       log.Printf("running %v", bed.Args)
-                       err := bed.Run()
-                       log.Printf("exited %v", bed.Args)
-                       if err != nil {
-                               errs <- fmt.Errorf("gvcf_regions: %s", err)
-                       }
-               }()
+               log.Printf("running %v", bed.Args)
+               err := bed.Run()
+               log.Printf("exited %v", bed.Args)
+               if err != nil {
+                       return fmt.Errorf("gvcf_regions: %s", err)
+               }
 
                // The bcftools --mask argument needs to end in ".bed"
                // in order to be parsed as a BED file, so we need to
@@ -266,7 +258,7 @@ func (cmd *vcf2fasta) vcf2fasta(infile string, phase int) error {
                        bedcompargs := []string{"bedtools", "complement", "-i", "/dev/stdin", "-g", cmd.genomeFile}
                        bedcompargs = maybeInDocker(bedcompargs, []string{cmd.genomeFile})
                        bedcomp := exec.Command(bedcompargs[0], bedcompargs[1:]...)
-                       bedcomp.Stdin = bedr
+                       bedcomp.Stdin = &regions
                        bedcomp.Stdout = maskfifow
                        bedcomp.Stderr = cmd.stderr
                        log.Printf("running %v", bedcomp.Args)