No issue #
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
chr2.241_254del 1 0
chr2.258_269delinsAA 1 0
chr2.315C>A 1 0
chr2.241_254del 1 0
chr2.258_269delinsAA 1 0
chr2.315C>A 1 0
chr2.471G>A 1 0
chr2.472G>A 1 0
`))
chr2.471G>A 1 0
chr2.472G>A 1 0
`))
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 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
`))
chr2 471 . G A . . . GT 0/1 0/0
chr2 472 . G A . . . GT 0/1 0/0
`))
chr2 240 . ATTTTTCTTGCTCTC A . . AC=1
chr2 258 . CCTTGTATTTTT AA . . AC=1
chr2 315 . C A . . AC=1
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
`))
chr2 471 . G A . . AC=1
chr2 472 . G A . . AC=1
`))
2,"chr2.241_254del"
3,"chr2.258_269delinsAA"
4,"chr2.315C>A"
2,"chr2.241_254del"
3,"chr2.258_269delinsAA"
4,"chr2.315C>A"
6,"chr2.471G>A"
7,"chr2.472G>A"
`)
6,"chr2.471G>A"
7,"chr2.472G>A"
`)
chr2:g.[241_254del];[241=] .
chr2:g.[258_269delinsAA];[258=] .
chr2:g.[315C>A];[315=] .
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] .
`))
chr2:g.[471=];[471G>A] .
chr2:g.[472=];[472G>A] .
`))
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 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
`))
chr2 471 . G A . . . GT 0/1 0/0
chr2 472 . G A . . . GT 0/1 0/0
`))
4,4,fe9a71a42adb4,chr2:g.125_127delinsAAA
6,6,e36dce85efbef,chr2:g.471G>A
6,6,e36dce85efbef,chr2:g.472G>A
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
pipeline1dup/input2 0
`), 0600)
c.Assert(err, check.IsNil)
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)
+
- exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
+ exited = (&sliceNumpy{}).RunCommand("slice-numpy", []string{
"-local=true",
"-chunked-hgvs-matrix=true",
"-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,
"-chi2-p-value=0.5",
"-min-coverage=0.75",
"-input-dir=" + slicedir,
pipeline1dup/input2 0
`), 0600)
c.Assert(err, check.IsNil)
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)
+
- exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
+ exited = (&sliceNumpy{}).RunCommand("slice-numpy", []string{
"-local=true",
"-chunked-onehot=true",
"-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,
"-chi2-p-value=0.5",
"-min-coverage=0.75",
"-input-dir=" + slicedir,
pipeline1dup/input2 0
`), 0600)
c.Assert(err, check.IsNil)
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)
+
- exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
+ exited = (&sliceNumpy{}).RunCommand("slice-numpy", []string{
"-local=true",
"-single-onehot=true",
"-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,
"-chi2-p-value=0.5",
"-min-coverage=0.75",
"-input-dir=" + slicedir,
spanningtile/input1 1
`), 0600)
c.Assert(err, check.IsNil)
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)
+
- exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
+ exited = (&sliceNumpy{}).RunCommand("slice-numpy", []string{
"-local=true",
"-chunked-hgvs-matrix=true",
"-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,
"-chi2-p-value=1",
"-min-coverage=0.75",
"-input-dir=" + slicedir,
spanningtile/input1 1
`), 0600)
c.Assert(err, check.IsNil)
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)
+
- exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
+ exited = (&sliceNumpy{}).RunCommand("slice-numpy", []string{
"-local=true",
"-chunked-onehot=true",
"-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,
"-chi2-p-value=1",
"-min-coverage=0.75",
"-input-dir=" + slicedir,
spanningtile/input1 1
`), 0600)
c.Assert(err, check.IsNil)
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)
+
- exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
+ exited = (&sliceNumpy{}).RunCommand("slice-numpy", []string{
"-local=true",
"-single-onehot=true",
"-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,
"-chi2-p-value=1",
"-min-coverage=0.75",
"-input-dir=" + slicedir,