Fix some tests.

[lightning.git] / slice_test.go

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,