Use tsv filename when using tab separator.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

diff --git a/export.go b/export.go
index 38fbeacb5283a96131ea5b4da3fa3216d9f780de..5e0ecf43e1889316e5ab3766667850bdaa34ce9e 100644 (file)
--- a/export.go
+++ b/export.go
@@ -44,8 +44,8 @@ var (
                "pvcf":        outputFormatPVCF,
                "vcf":         outputFormatVCF,
        }
-       outputFormatHGVS       = outputFormat{Filename: "out.csv", Head: headNone, Print: printHGVS}
-       outputFormatHGVSOneHot = outputFormat{Filename: "out.csv", Head: headNone, Print: printHGVSOneHot}
+       outputFormatHGVS       = outputFormat{Filename: "out.tsv", Head: headNone, Print: printHGVS}
+       outputFormatHGVSOneHot = outputFormat{Filename: "out.tsv", Head: headNone, Print: printHGVSOneHot}
        outputFormatPVCF       = outputFormat{Filename: "out.vcf", Head: headPVCF, Print: printPVCF, PadLeft: true}
        outputFormatVCF        = outputFormat{Filename: "out.vcf", Head: headVCF, Print: printVCF, PadLeft: true}
        headNone               = func(io.Writer, []CompactGenome) {}

diff --git a/export_test.go b/export_test.go
index 0971a155bcf639fa0d349c67953474060d5c6e05..2b7772c3829fc07f15c9b875cb4216bc7f8c0b01 100644 (file)
--- a/export_test.go
+++ b/export_test.go
@@ -4,6 +4,7 @@ import (
        "bytes"
        "io/ioutil"
        "os"
+       "os/exec"
 
        "gopkg.in/check.v1"
 )
@@ -32,8 +33,11 @@ func (s *exportSuite) TestFastaToHGVS(c *check.C) {
                "-ref=testdata/ref.fasta",
        }, &buffer, os.Stderr, os.Stderr)
        c.Check(exited, check.Equals, 0)
-       output, err := ioutil.ReadFile(tmpdir + "/out.chr1.csv")
-       c.Check(err, check.IsNil)
+       output, err := ioutil.ReadFile(tmpdir + "/out.chr1.tsv")
+       if !c.Check(err, check.IsNil) {
+               out, _ := exec.Command("find", tmpdir, "-ls").CombinedOutput()
+               c.Logf("%s", out)
+       }
        c.Check(sortLines(string(output)), check.Equals, sortLines(`chr1.1_3delinsGGC   1       0
 chr1.41_42delinsAA     1       0
 chr1.161A>T    1       0
@@ -41,7 +45,7 @@ chr1.178A>T   1       0
 chr1.222_224del        1       0
 chr1.302_305delinsAAAA 1       0
 `))
-       output, err = ioutil.ReadFile(tmpdir + "/out.chr2.csv")
+       output, err = ioutil.ReadFile(tmpdir + "/out.chr2.tsv")
        c.Check(err, check.IsNil)
        c.Check(sortLines(string(output)), check.Equals, sortLines(`chr2.1_3delinsAAA   0       1
 chr2.125_127delinsAAA  0       1
@@ -53,8 +57,8 @@ chr2.471_472delinsAA  1       0
 `))
        labels, err := ioutil.ReadFile(tmpdir + "/labels.csv")
        c.Check(err, check.IsNil)
-       c.Check(string(labels), check.Equals, `0,"input1","out.csv"
-1,"input2","out.csv"
+       c.Check(string(labels), check.Equals, `0,"input1","out.tsv"
+1,"input2","out.tsv"
 `)
 
        exited = (&exporter{}).RunCommand("export", []string{

diff --git a/pipeline_test.go b/pipeline_test.go
index e1b6427c2f3a4200c0d387cdd0d7f01bcfdc62b2..eecc30490628ec839658525058144c5ec68c3f3f 100644 (file)
--- a/pipeline_test.go
+++ b/pipeline_test.go
@@ -89,7 +89,7 @@ func (s *pipelineSuite) TestImportMerge(c *check.C) {
 
        code = (&exporter{}).RunCommand("lightning export", []string{"-local", "-ref", "testdata/ref.fasta", "-output-format", "hgvs", "-input-dir", tmpdir + "/merged", "-output-dir", tmpdir, "-output-per-chromosome=false"}, bytes.NewReader(nil), os.Stderr, os.Stderr)
        c.Check(code, check.Equals, 0)
-       hgvsout, err := ioutil.ReadFile(tmpdir + "/out.csv")
+       hgvsout, err := ioutil.ReadFile(tmpdir + "/out.tsv")
        c.Check(err, check.IsNil)
        c.Check(sortLines(string(hgvsout)), check.Equals, sortLines(`chr1:g.1_3delinsGGC        .
 chr1:g.[41_42delinsAA];[41=]   .