Use buffered writer to avoid overwhelming arv-mount.

[lightning.git] / pipeline_test.go

diff --git a/pipeline_test.go b/pipeline_test.go
index 49dc39ddacf386cf89afa68591b8fa7d2153bbea..c917b3610de4f8dcf7181d4ebfe04c012c2cb95f 100644 (file)
--- a/pipeline_test.go
+++ b/pipeline_test.go
@@ -63,7 +63,7 @@ func (s *pipelineSuite) TestImportMerge(c *check.C) {
                        args := []string{"-local=true", "-o=" + libfile[i], "-skip-ooo=true", "-output-tiles", "-tag-library", "testdata/tags"}
                        if i == 0 {
                                // ref only
-                               args = append(args, "-include-no-calls")
+                               args = append(args, "-save-incomplete-tiles")
                        }
                        args = append(args, infile)
                        code := (&importer{}).RunCommand("lightning import", args, bytes.NewReader(nil), &bytes.Buffer{}, os.Stderr)
@@ -127,7 +127,7 @@ chr2        471     GG      AA      0/1     0/0
        bedout, err := ioutil.ReadFile(tmpdir + "/export.bed")
        c.Check(err, check.IsNil)
        c.Logf("%s", string(bedout))
-       c.Check(string(bedout), check.Equals, `chr1 0 248 0 500 . 0 224
+       c.Check(string(bedout), check.Equals, `chr1 0 248 0 1000 . 0 224
 chr1 224 372 1 1000 . 248 348
 chr1 348 496 2 1000 . 372 472
 chr1 472 572 3 1000 . 496 572
@@ -143,21 +143,21 @@ chr2 472 572 7 1000 . 496 572
        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
+       c.Check(sorted, check.Equals, sortLines(`0,8d4fe9a63921b,chr1:g.161A>T
+0,8d4fe9a63921b,chr1:g.178A>T
+0,8d4fe9a63921b,chr1:g.1_3delinsGGC
+0,8d4fe9a63921b,chr1:g.222_224del
+0,ba4263ca4199c,chr1:g.1_3delinsGGC
+0,ba4263ca4199c,chr1:g.222_224del
+0,ba4263ca4199c,chr1:g.41_42delinsAA
+1,139890345dbb8,chr1:g.302_305delinsAAAA
+4,cbfca15d241d3,chr2:g.125_127delinsAAA
+4,cbfca15d241d3,chr2:g.1_3delinsAAA
+4,f5fafe9450b02,chr2:g.241_245delinsAAAAA
+4,f5fafe9450b02,chr2:g.291C>A
+4,fe9a71a42adb4,chr2:g.125_127delinsAAA
+6,e36dce85efbef,chr2:g.471_472delinsAA
+6,f81388b184f4a,chr2:g.470_472del
 `))
 }