From: Tom Clegg <tom@tomclegg.ca>
Date: Wed, 25 Nov 2020 20:50:16 +0000 (-0500)
Subject: Use buffered writer to avoid overwhelming arv-mount.
X-Git-Url: https://git.arvados.org/lightning.git/commitdiff_plain/76fbc75a359348e2a91546a70b8d2c738865cce2

Use buffered writer to avoid overwhelming arv-mount.

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

diff --git a/vcf2fasta.go b/vcf2fasta.go
index 98b285e0ed..08eedf9446 100644
--- a/vcf2fasta.go
+++ b/vcf2fasta.go
@@ -236,7 +236,8 @@ func (cmd *vcf2fasta) vcf2fasta(infile string, phase int) error {
 		return fmt.Errorf("error opening output file: %s", err)
 	}
 	defer outf.Close()
-	gzipw := gzip.NewWriter(outf)
+	bufw := bufio.NewWriterSize(outf, 8*1024*1024)
+	gzipw := gzip.NewWriter(bufw)
 	defer gzipw.Close()
 
 	var maskfifo string // filename of mask fifo if we're running bedtools, otherwise ""
@@ -419,11 +420,17 @@ func (cmd *vcf2fasta) vcf2fasta(infile string, phase int) error {
 			errs <- fmt.Errorf("bcftools consensus: %s", err)
 			return
 		}
+		log.Printf("exited %v", consensus.Args)
 		err = gzipw.Close()
 		if err != nil {
 			errs <- err
 			return
 		}
+		err = bufw.Flush()
+		if err != nil {
+			errs <- err
+			return
+		}
 		errs <- outf.Close()
 	}()