Fix some tests.

No issue #

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

diff --git a/export_test.go b/export_test.go
index f904e76f4a8d5838f450ee542e84b286ba4c5f1f..15278bea29d937b712015bb00bf9db6c743a4eda 100644 (file)
--- a/export_test.go
+++ b/export_test.go
@@ -82,7 +82,7 @@ chr2.125_127delinsAAA 0       1
 chr2.241_254del        1       0
 chr2.258_269delinsAA   1       0
 chr2.315C>A    1       0
-chr2.470_472del        1       0
+chr2.469_471del        1       0
 chr2.471G>A    1       0
 chr2.472G>A    1       0
 `))
@@ -123,7 +123,7 @@ 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   468     .       CGTG    C       .       .       .       GT      1/0     0/0
 chr2   471     .       G       A       .       .       .       GT      0/1     0/0
 chr2   472     .       G       A       .       .       .       GT      0/1     0/0
 `))
@@ -157,7 +157,7 @@ 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   468     .       CGTG    C       .       .       AC=1
 chr2   471     .       G       A       .       .       AC=1
 chr2   472     .       G       A       .       .       AC=1
 `))
@@ -218,7 +218,7 @@ chr2        472     .       G       A       .       .       AC=1
 2,"chr2.241_254del"
 3,"chr2.258_269delinsAA"
 4,"chr2.315C>A"
-5,"chr2.470_472del"
+5,"chr2.469_471del"
 6,"chr2.471G>A"
 7,"chr2.472G>A"
 `)

diff --git a/pipeline_test.go b/pipeline_test.go
index 391312e507fa6315e3f4cd051822810990fb744e..606cac243d32c2c0f505ff3fe7becf8cce136455 100644 (file)
--- a/pipeline_test.go
+++ b/pipeline_test.go
@@ -107,7 +107,7 @@ chr1:g.[302=];[302_305delinsAAAA]   .
 chr2:g.[241_254del];[241=]     .
 chr2:g.[258_269delinsAA];[258=]        .
 chr2:g.[315C>A];[315=] .
-chr2:g.[470_472del];[470=]     .
+chr2:g.[469_471del];[469=]     .
 chr2:g.[471=];[471G>A] .
 chr2:g.[472=];[472G>A] .
 `))
@@ -130,7 +130,7 @@ 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   468     .       CGTG    C       .       .       .       GT      1/0     0/0
 chr2   471     .       G       A       .       .       .       GT      0/1     0/0
 chr2   472     .       G       A       .       .       .       GT      0/1     0/0
 `))
@@ -169,7 +169,7 @@ chr2 472 572 7 1000 . 496 572
 4,4,fe9a71a42adb4,chr2:g.125_127delinsAAA
 6,6,e36dce85efbef,chr2:g.471G>A
 6,6,e36dce85efbef,chr2:g.472G>A
-6,6,f81388b184f4a,chr2:g.470_472del
+6,6,f81388b184f4a,chr2:g.469_471del
 `))
 }
 

diff --git a/slice_test.go b/slice_test.go
index ec879589954eb5f9e04c38a0fc0805c0b88fb6e5..7b81e0ec661ca75f9147a239aa86bb1e24432d77 100644 (file)
--- a/slice_test.go
+++ b/slice_test.go
@@ -244,12 +244,21 @@ pipeline1dup/input1       1
 pipeline1dup/input2    0
 `), 0600)
                c.Assert(err, check.IsNil)
+
+               exited := (&chooseSamples{}).RunCommand("choose-samples", []string{
+                       "-local=true",
+                       "-case-control-file=" + tmpdir + "/casecontrol.tsv",
+                       "-case-control-column=CC",
+                       "-input-dir=" + slicedir,
+                       "-output-dir=" + tmpdir,
+               }, nil, os.Stderr, os.Stderr)
+               c.Check(exited, check.Equals, 0)
+
                npydir := c.MkDir()
-               exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
+               exited = (&sliceNumpy{}).RunCommand("slice-numpy", []string{
                        "-local=true",
                        "-chunked-hgvs-matrix=true",
-                       "-chi2-case-control-file=" + tmpdir + "/casecontrol.tsv",
-                       "-chi2-case-control-column=CC",
+                       "-samples=" + tmpdir + "/samples.csv",
                        "-chi2-p-value=0.5",
                        "-min-coverage=0.75",
                        "-input-dir=" + slicedir,
@@ -280,12 +289,21 @@ pipeline1dup/input1       1
 pipeline1dup/input2    0
 `), 0600)
                c.Assert(err, check.IsNil)
+
+               exited := (&chooseSamples{}).RunCommand("choose-samples", []string{
+                       "-local=true",
+                       "-case-control-file=" + tmpdir + "/casecontrol.tsv",
+                       "-case-control-column=CC",
+                       "-input-dir=" + slicedir,
+                       "-output-dir=" + tmpdir,
+               }, nil, os.Stderr, os.Stderr)
+               c.Check(exited, check.Equals, 0)
+
                npydir := c.MkDir()
-               exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
+               exited = (&sliceNumpy{}).RunCommand("slice-numpy", []string{
                        "-local=true",
                        "-chunked-onehot=true",
-                       "-chi2-case-control-file=" + tmpdir + "/casecontrol.tsv",
-                       "-chi2-case-control-column=CC",
+                       "-samples=" + tmpdir + "/samples.csv",
                        "-chi2-p-value=0.5",
                        "-min-coverage=0.75",
                        "-input-dir=" + slicedir,
@@ -324,12 +342,21 @@ pipeline1dup/input1       1
 pipeline1dup/input2    0
 `), 0600)
                c.Assert(err, check.IsNil)
+
+               exited := (&chooseSamples{}).RunCommand("choose-samples", []string{
+                       "-local=true",
+                       "-case-control-file=" + tmpdir + "/casecontrol.tsv",
+                       "-case-control-column=CC",
+                       "-input-dir=" + slicedir,
+                       "-output-dir=" + tmpdir,
+               }, nil, os.Stderr, os.Stderr)
+               c.Check(exited, check.Equals, 0)
+
                npydir := c.MkDir()
-               exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
+               exited = (&sliceNumpy{}).RunCommand("slice-numpy", []string{
                        "-local=true",
                        "-single-onehot=true",
-                       "-chi2-case-control-file=" + tmpdir + "/casecontrol.tsv",
-                       "-chi2-case-control-column=CC",
+                       "-samples=" + tmpdir + "/samples.csv",
                        "-chi2-p-value=0.5",
                        "-min-coverage=0.75",
                        "-input-dir=" + slicedir,
@@ -580,12 +607,21 @@ func (s *sliceSuite) TestSpanningTile(c *check.C) {
 spanningtile/input1    1
 `), 0600)
                c.Assert(err, check.IsNil)
+
+               exited := (&chooseSamples{}).RunCommand("choose-samples", []string{
+                       "-local=true",
+                       "-case-control-file=" + tmpdir + "/casecontrol.tsv",
+                       "-case-control-column=CC",
+                       "-input-dir=" + slicedir,
+                       "-output-dir=" + tmpdir,
+               }, nil, os.Stderr, os.Stderr)
+               c.Check(exited, check.Equals, 0)
+
                npydir := c.MkDir()
-               exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
+               exited = (&sliceNumpy{}).RunCommand("slice-numpy", []string{
                        "-local=true",
                        "-chunked-hgvs-matrix=true",
-                       "-chi2-case-control-file=" + tmpdir + "/casecontrol.tsv",
-                       "-chi2-case-control-column=CC",
+                       "-samples=" + tmpdir + "/samples.csv",
                        "-chi2-p-value=1",
                        "-min-coverage=0.75",
                        "-input-dir=" + slicedir,
@@ -607,12 +643,21 @@ spanningtile/input1       1
 spanningtile/input1    1
 `), 0600)
                c.Assert(err, check.IsNil)
+
+               exited := (&chooseSamples{}).RunCommand("choose-samples", []string{
+                       "-local=true",
+                       "-case-control-file=" + tmpdir + "/casecontrol.tsv",
+                       "-case-control-column=CC",
+                       "-input-dir=" + slicedir,
+                       "-output-dir=" + tmpdir,
+               }, nil, os.Stderr, os.Stderr)
+               c.Check(exited, check.Equals, 0)
+
                npydir := c.MkDir()
-               exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
+               exited = (&sliceNumpy{}).RunCommand("slice-numpy", []string{
                        "-local=true",
                        "-chunked-onehot=true",
-                       "-chi2-case-control-file=" + tmpdir + "/casecontrol.tsv",
-                       "-chi2-case-control-column=CC",
+                       "-samples=" + tmpdir + "/samples.csv",
                        "-chi2-p-value=1",
                        "-min-coverage=0.75",
                        "-input-dir=" + slicedir,
@@ -645,12 +690,21 @@ spanningtile/input1       1
 spanningtile/input1    1
 `), 0600)
                c.Assert(err, check.IsNil)
+
+               exited := (&chooseSamples{}).RunCommand("choose-samples", []string{
+                       "-local=true",
+                       "-case-control-file=" + tmpdir + "/casecontrol.tsv",
+                       "-case-control-column=CC",
+                       "-input-dir=" + slicedir,
+                       "-output-dir=" + tmpdir,
+               }, nil, os.Stderr, os.Stderr)
+               c.Check(exited, check.Equals, 0)
+
                npydir := c.MkDir()
-               exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
+               exited = (&sliceNumpy{}).RunCommand("slice-numpy", []string{
                        "-local=true",
                        "-single-onehot=true",
-                       "-chi2-case-control-file=" + tmpdir + "/casecontrol.tsv",
-                       "-chi2-case-control-column=CC",
+                       "-samples=" + tmpdir + "/samples.csv",
                        "-chi2-p-value=1",
                        "-min-coverage=0.75",
                        "-input-dir=" + slicedir,