Separate pvcf/vcf output.

[lightning.git] / export_test.go

diff --git a/export_test.go b/export_test.go
index 8ee3ab48ef66e7e1c589f0d88ee3095356fdab82..c3a0b845bdc063201dab37b622a65d21ab64475d 100644 (file)
--- a/export_test.go
+++ b/export_test.go
@@ -57,6 +57,36 @@ chr2.471_472delinsAA 1       0
 1,"input2","out.csv"
 `)
 
+       exited = (&exporter{}).RunCommand("export", []string{
+               "-local=true",
+               "-input-dir=" + tmpdir,
+               "-output-dir=" + tmpdir,
+               "-output-format=pvcf",
+               "-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     .       .       GT      1/1     0/0
+chr1   41      TT      AA      .       .       GT      1/0     0/0
+chr1   161     A       T       .       .       GT      0/1     0/0
+chr1   178     A       T       .       .       GT      0/1     0/0
+chr1   221     TCCA    T       .       .       GT      1/1     0/0
+chr1   302     TTTT    AAAA    .       .       GT      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     .       .       GT      0/0     0/1
+chr2   125     CTT     AAA     .       .       GT      0/0     1/1
+chr2   240     ATTTTTCTTGCTCTC A       .       .       GT      1/0     0/0
+chr2   258     CCTTGTATTTTT    AA      .       .       GT      1/0     0/0
+chr2   315     C       A       .       .       GT      1/0     0/0
+chr2   469     GTGG    G       .       .       GT      1/0     0/0
+chr2   471     GG      AA      .       .       GT      0/1     0/0
+`))
+
        exited = (&exporter{}).RunCommand("export", []string{
                "-local=true",
                "-input-dir=" + tmpdir,
@@ -68,22 +98,22 @@ chr2.471_472delinsAA        1       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
+       c.Check(sortLines(string(output)), check.Equals, sortLines(`chr1        1       NNN     GGC     .       .       AC=2    GT      0/1
+chr1   41      TT      AA      .       .       AC=1    GT      0/1
+chr1   161     A       T       .       .       AC=1    GT      0/1
+chr1   178     A       T       .       .       AC=1    GT      0/1
+chr1   221     TCCA    T       .       .       AC=2    GT      0/1
+chr1   302     TTTT    AAAA    .       .       AC=1    GT      0/1
 `))
        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
+       c.Check(sortLines(string(output)), check.Equals, sortLines(`chr2        1       TTT     AAA     .       .       AC=1    GT      0/1
+chr2   125     CTT     AAA     .       .       AC=2    GT      0/1
+chr2   240     ATTTTTCTTGCTCTC A       .       .       AC=1    GT      0/1
+chr2   258     CCTTGTATTTTT    AA      .       .       AC=1    GT      0/1
+chr2   315     C       A       .       .       AC=1    GT      0/1
+chr2   469     GTGG    G       .       .       AC=1    GT      0/1
+chr2   471     GG      AA      .       .       AC=1    GT      0/1
 `))
 }