Update test.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

diff --git a/pipeline_test.go b/pipeline_test.go
index 2b0f3933126223ae19f7c8ac40c5ff11baece9ca..44440962a9ab549111bfdeedb64c5b4e2f054ced 100644 (file)
--- a/pipeline_test.go
+++ b/pipeline_test.go
@@ -88,17 +88,19 @@ 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
-chr1:g.[41_42delinsAA];[41=]
-chr1:g.[161=];[161A>T]
-chr1:g.[178=];[178A>T]
-chr1:g.222_224del
-chr1:g.[302=];[302_305delinsAAAA]
-chr2:g.[813_826del];[813=]
-chr2:g.[830_841delinsAA];[830=]
-chr2:g.[887C>A];[887=]
-chr2:g.[1042_1044del];[1042=]
-chr2:g.[1043=];[1043_1044delinsAA]
+       c.Check(hgvsout.String(), check.Equals, `chr1:g.1_3delinsGGC    .
+chr1:g.[41_42delinsAA];[41=]   .
+chr1:g.[161=];[161A>T] .
+chr1:g.[178=];[178A>T] .
+chr1:g.222_224del      .
+chr1:g.[302=];[302_305delinsAAAA]      .
+.      chr2:g.[1=];[1_3delinsAAA]
+.      chr2:g.125_127delinsAAA
+chr2:g.[241_254del];[241=]     .
+chr2:g.[258_269delinsAA];[258=]        .
+chr2:g.[315C>A];[315=] .
+chr2:g.[470_472del];[470=]     .
+chr2:g.[471=];[471_472delinsAA]        .
 `)
 
        vcfout := &bytes.Buffer{}
@@ -106,28 +108,30 @@ chr2:g.[1043=];[1043_1044delinsAA]
        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
-chr1   41      TT      AA      1/0
-chr1   161     A       T       0/1
-chr1   178     A       T       0/1
-chr1   221     TCCA    T       1/1
-chr1   302     TTTT    AAAA    0/1
-chr2   812     ATTTTTCTTGCTCTC A       1/0
-chr2   830     CCTTGTATTTTT    AA      1/0
-chr2   887     C       A       1/0
-chr2   1041    GTGG    G       1/0
-chr2   1043    GG      AA      0/1
+       c.Check(vcfout.String(), check.Equals, `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
+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
 `)
        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 1000 . 0 224
-chr1 224 372 1 500 . 248 348
+       c.Check(string(bedout), check.Equals, `chr1 0 248 0 500 . 0 224
+chr1 224 372 1 250 . 248 348
 chr1 348 496 2 0 . 372 472
 chr1 472 572 3 0 . 496 572
-chr2 572 820 4 500 . 0 796
-chr2 796 944 5 0 . 820 920
-chr2 920 1068 6 1000 . 944 1044
-chr2 1044 1144 7 0 . 1068 1144
+chr2 0 248 4 750 . 0 224
+chr2 224 372 5 0 . 248 348
+chr2 348 496 6 500 . 372 472
+chr2 472 572 7 0 . 496 572
 `)
 }