Export tile annotations.

[lightning.git] / pipeline_test.go

diff --git a/pipeline_test.go b/pipeline_test.go
index bf6cf5597c590ae8a8cd4a0c5a612c22f612f3d1..49dc39ddacf386cf89afa68591b8fa7d2153bbea 100644 (file)
--- a/pipeline_test.go
+++ b/pipeline_test.go
@@ -6,6 +6,8 @@ import (
        "io"
        "io/ioutil"
        "os"
+       "sort"
+       "strings"
        "sync"
 
        "gopkg.in/check.v1"
@@ -134,4 +136,33 @@ chr2 224 372 5 750 . 248 348
 chr2 348 496 6 1000 . 372 472
 chr2 472 572 7 1000 . 496 572
 `)
+
+       annotateout := &bytes.Buffer{}
+       code = (&annotatecmd{}).RunCommand("lightning annotate", []string{"-local", "-variant-hash=true", "-i", tmpdir + "/merged.gob"}, bytes.NewReader(nil), annotateout, os.Stderr)
+       c.Check(code, check.Equals, 0)
+       c.Check(annotateout.Len() > 0, check.Equals, true)
+       sorted := sortLines(annotateout.String())
+       c.Logf("%s", sorted)
+       c.Check(sorted, check.Equals, sortLines(`0      8d4fe9a63921b   testdata/ref.fasta      chr1:g.161A>T
+0      8d4fe9a63921b   testdata/ref.fasta      chr1:g.178A>T
+0      8d4fe9a63921b   testdata/ref.fasta      chr1:g.1_3delinsGGC
+0      8d4fe9a63921b   testdata/ref.fasta      chr1:g.222_224del
+0      ba4263ca4199c   testdata/ref.fasta      chr1:g.1_3delinsGGC
+0      ba4263ca4199c   testdata/ref.fasta      chr1:g.222_224del
+0      ba4263ca4199c   testdata/ref.fasta      chr1:g.41_42delinsAA
+1      139890345dbb8   testdata/ref.fasta      chr1:g.302_305delinsAAAA
+4      cbfca15d241d3   testdata/ref.fasta      chr2:g.125_127delinsAAA
+4      cbfca15d241d3   testdata/ref.fasta      chr2:g.1_3delinsAAA
+4      f5fafe9450b02   testdata/ref.fasta      chr2:g.241_245delinsAAAAA
+4      f5fafe9450b02   testdata/ref.fasta      chr2:g.291C>A
+4      fe9a71a42adb4   testdata/ref.fasta      chr2:g.125_127delinsAAA
+6      e36dce85efbef   testdata/ref.fasta      chr2:g.471_472delinsAA
+6      f81388b184f4a   testdata/ref.fasta      chr2:g.470_472del
+`))
+}
+
+func sortLines(txt string) string {
+       lines := strings.Split(strings.TrimRightFunc(txt, func(c rune) bool { return c == '\n' }), "\n")
+       sort.Strings(lines)
+       return strings.Join(lines, "\n") + "\n"
 }