Fix up VCF format.

[lightning.git] / export_test.go

diff --git a/export_test.go b/export_test.go
index c3a0b845bdc063201dab37b622a65d21ab64475d..0971a155bcf639fa0d349c67953474060d5c6e05 100644 (file)
--- a/export_test.go
+++ b/export_test.go
@@ -68,23 +68,27 @@ 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     .       .       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
+       c.Check(sortLines(string(output)), check.Equals, sortLines(`##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+#CHROM POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  testdata/pipeline1/input1.1.fasta       testdata/pipeline1/input2.1.fasta
+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
+       c.Check(sortLines(string(output)), check.Equals, sortLines(`##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+#CHROM POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  testdata/pipeline1/input1.1.fasta       testdata/pipeline1/input2.1.fasta
+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{
@@ -98,22 +102,24 @@ chr2       471     GG      AA      .       .       GT      0/1     0/0
        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     .       .       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
+       c.Check(sortLines(string(output)), check.Equals, sortLines(`#CHROM      POS     ID      REF     ALT     QUAL    FILTER  INFO
+chr1   1       .       NNN     GGC     .       .       AC=2
+chr1   41      .       TT      AA      .       .       AC=1
+chr1   161     .       A       T       .       .       AC=1
+chr1   178     .       A       T       .       .       AC=1
+chr1   221     .       TCCA    T       .       .       AC=2
+chr1   302     .       TTTT    AAAA    .       .       AC=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     .       .       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
+       c.Check(sortLines(string(output)), check.Equals, sortLines(`#CHROM      POS     ID      REF     ALT     QUAL    FILTER  INFO
+chr2   1       .       TTT     AAA     .       .       AC=1
+chr2   125     .       CTT     AAA     .       .       AC=2
+chr2   240     .       ATTTTTCTTGCTCTC A       .       .       AC=1
+chr2   258     .       CCTTGTATTTTT    AA      .       .       AC=1
+chr2   315     .       C       A       .       .       AC=1
+chr2   469     .       GTGG    G       .       .       AC=1
+chr2   471     .       GG      AA      .       .       AC=1
 `))
 }