From fab96d7f0f6c1564b6ed376c0e253c59f343dc09 Mon Sep 17 00:00:00 2001 From: Tom Clegg Date: Fri, 30 Jul 2021 09:20:00 -0400 Subject: [PATCH] Use tsv filename when using tab separator. Arvados-DCO-1.1-Signed-off-by: Tom Clegg --- export.go | 4 ++-- export_test.go | 14 +++++++++----- pipeline_test.go | 2 +- 3 files changed, 12 insertions(+), 8 deletions(-) diff --git a/export.go b/export.go index 38fbeacb52..5e0ecf43e1 100644 --- 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 0971a155bc..2b7772c382 100644 --- 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 e1b6427c2f..eecc304906 100644 --- 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=] . -- 2.30.2