Fixup multiple-file reading.

[lightning.git] / pipeline_test.go

diff --git a/pipeline_test.go b/pipeline_test.go
index 49dc39ddacf386cf89afa68591b8fa7d2153bbea..67fff89fb6717405858e37858cf6720a74313fcf 100644 (file)
--- a/pipeline_test.go
+++ b/pipeline_test.go
@@ -1,4 +1,4 @@
-package main
+package lightning
 
 import (
        "bytes"
@@ -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)
@@ -90,7 +90,7 @@ func (s *pipelineSuite) TestImportMerge(c *check.C) {
        c.Check(code, check.Equals, 0)
        c.Check(hgvsout.Len() > 0, check.Equals, true)
        c.Logf("%s", hgvsout.String())
-       c.Check(hgvsout.String(), check.Equals, `chr1:g.1_3delinsGGC    .
+       c.Check(sortLines(hgvsout.String()), check.Equals, sortLines(`chr1:g.1_3delinsGGC       .
 chr1:g.[41_42delinsAA];[41=]   .
 chr1:g.[161=];[161A>T] .
 chr1:g.[178=];[178A>T] .
@@ -103,14 +103,14 @@ chr2:g.[258_269delinsAA];[258=]   .
 chr2:g.[315C>A];[315=] .
 chr2:g.[470_472del];[470=]     .
 chr2:g.[471=];[471_472delinsAA]        .
-`)
+`))
 
        vcfout := &bytes.Buffer{}
        code = (&exporter{}).RunCommand("lightning export", []string{"-local", "-ref", "testdata/ref.fasta", "-output-format", "vcf", "-i", tmpdir + "/merged.gob", "-output-bed", tmpdir + "/export.bed"}, bytes.NewReader(nil), vcfout, os.Stderr)
        c.Check(code, check.Equals, 0)
        c.Check(vcfout.Len() > 0, check.Equals, true)
        c.Logf("%s", vcfout.String())
-       c.Check(vcfout.String(), check.Equals, `chr1    1       NNN     GGC     1/1     0/0
+       c.Check(sortLines(vcfout.String()), 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
@@ -123,11 +123,11 @@ 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
-`)
+`))
        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(sortLines(string(bedout)), check.Equals, sortLines(`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
@@ -135,7 +135,7 @@ chr2 0 248 4 1000 . 0 224
 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)
@@ -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(`0,0,8d4fe9a63921b,chr1:g.161A>T
+0,0,8d4fe9a63921b,chr1:g.178A>T
+0,0,8d4fe9a63921b,chr1:g.1_3delinsGGC
+0,0,8d4fe9a63921b,chr1:g.222_224del
+0,0,ba4263ca4199c,chr1:g.1_3delinsGGC
+0,0,ba4263ca4199c,chr1:g.222_224del
+0,0,ba4263ca4199c,chr1:g.41_42delinsAA
+1,1,139890345dbb8,chr1:g.302_305delinsAAAA
+4,4,cbfca15d241d3,chr2:g.125_127delinsAAA
+4,4,cbfca15d241d3,chr2:g.1_3delinsAAA
+4,4,f5fafe9450b02,chr2:g.241_245delinsAAAAA
+4,4,f5fafe9450b02,chr2:g.291C>A
+4,4,fe9a71a42adb4,chr2:g.125_127delinsAAA
+6,6,e36dce85efbef,chr2:g.471_472delinsAA
+6,6,f81388b184f4a,chr2:g.470_472del
 `))
 }