From 5ac2b976e35a118e90535390a22912fc06c7b53f Mon Sep 17 00:00:00 2001
From: Tom Clegg <tom@tomclegg.ca>
Date: Thu, 8 Jul 2021 19:06:07 -0400
Subject: [PATCH] Fix missing output.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
---
 export.go      |  5 +++--
 export_test.go | 31 +++++++++++++++++++++++++++++++
 2 files changed, 34 insertions(+), 2 deletions(-)

diff --git a/export.go b/export.go
index e22e04a291..8d455b15ac 100644
--- a/export.go
+++ b/export.go
@@ -138,7 +138,7 @@ func (cmd *exporter) RunCommand(prog string, args []string, stdin io.Reader, std
 		if err != nil {
 			return 1
 		}
-		fmt.Fprintln(stdout, output+"/export.csv")
+		fmt.Fprintln(stdout, output)
 		return 0
 	}
 
@@ -304,13 +304,14 @@ func (cmd *exporter) export(outdir string, bedout io.Writer, tilelib *tileLibrar
 				defer bedw.Close()
 			}
 			defer outw.Close()
-			outwb := bufio.NewWriter(outw)
+			outwb := bufio.NewWriterSize(outw, 8*1024*1024)
 			defer outwb.Flush()
 			cmd.exportSeq(outwb, bedw, tilelib.taglib.keylen, seqname, refseq[seqname], tilelib, cgs)
 		}()
 	}
 
 	merges.Wait()
+	throttle.Wait()
 	return nil
 }
 
diff --git a/export_test.go b/export_test.go
index 1dc2ad87b6..8ee3ab48ef 100644
--- a/export_test.go
+++ b/export_test.go
@@ -22,6 +22,7 @@ func (s *exportSuite) TestFastaToHGVS(c *check.C) {
 	exited := (&importer{}).RunCommand("import", []string{"-local=true", "-tag-library", "testdata/tags", "-output-tiles", "-save-incomplete-tiles", "testdata/pipeline1", "testdata/ref.fasta"}, &bytes.Buffer{}, &buffer, os.Stderr)
 	c.Assert(exited, check.Equals, 0)
 	ioutil.WriteFile(tmpdir+"/library.gob", buffer.Bytes(), 0644)
+
 	exited = (&exporter{}).RunCommand("export", []string{
 		"-local=true",
 		"-input-dir=" + tmpdir,
@@ -55,4 +56,34 @@ chr2.471_472delinsAA	1	0
 	c.Check(string(labels), check.Equals, `0,"input1","out.csv"
 1,"input2","out.csv"
 `)
+
+	exited = (&exporter{}).RunCommand("export", []string{
+		"-local=true",
+		"-input-dir=" + tmpdir,
+		"-output-dir=" + tmpdir,
+		"-output-format=vcf",
+		"-ref=testdata/ref.fasta",
+	}, &buffer, os.Stderr, os.Stderr)
+	c.Check(exited, check.Equals, 0)
+	output, err = ioutil.ReadFile(tmpdir + "/out.chr1.vcf")
+	c.Check(err, check.IsNil)
+	c.Log(string(output))
+	c.Check(sortLines(string(output)), check.Equals, sortLines(`chr1	1	NNN	GGC	1/1	0/0
+chr1	41	TT	AA	1/0	0/0
+chr1	161	A	T	0/1	0/0
+chr1	178	A	T	0/1	0/0
+chr1	221	TCCA	T	1/1	0/0
+chr1	302	TTTT	AAAA	0/1	0/0
+`))
+	output, err = ioutil.ReadFile(tmpdir + "/out.chr2.vcf")
+	c.Check(err, check.IsNil)
+	c.Log(string(output))
+	c.Check(sortLines(string(output)), check.Equals, sortLines(`chr2	1	TTT	AAA	0/0	0/1
+chr2	125	CTT	AAA	0/0	1/1
+chr2	240	ATTTTTCTTGCTCTC	A	1/0	0/0
+chr2	258	CCTTGTATTTTT	AA	1/0	0/0
+chr2	315	C	A	1/0	0/0
+chr2	469	GTGG	G	1/0	0/0
+chr2	471	GG	AA	0/1	0/0
+`))
 }
-- 
2.30.2