X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/6104156cf02739811670759b77307fdfeaca38d6..HEAD:/slice_test.go

diff --git a/slice_test.go b/slice_test.go
deleted file mode 100644
index ec87958995..0000000000
--- a/slice_test.go
+++ /dev/null
@@ -1,750 +0,0 @@
-// Copyright (C) The Lightning Authors. All rights reserved.
-//
-// SPDX-License-Identifier: AGPL-3.0
-
-package lightning
-
-import (
-	"io/ioutil"
-	"os"
-	"os/exec"
-
-	"github.com/kshedden/gonpy"
-	"gopkg.in/check.v1"
-)
-
-type sliceSuite struct{}
-
-var _ = check.Suite(&sliceSuite{})
-
-func (s *sliceSuite) TestImportAndSlice(c *check.C) {
-	tmpdir := c.MkDir()
-	err := os.Mkdir(tmpdir+"/lib1", 0777)
-	c.Assert(err, check.IsNil)
-	err = os.Mkdir(tmpdir+"/lib2", 0777)
-	c.Assert(err, check.IsNil)
-	err = os.Mkdir(tmpdir+"/lib3", 0777)
-	c.Assert(err, check.IsNil)
-	cwd, err := os.Getwd()
-	c.Assert(err, check.IsNil)
-	err = os.Symlink(cwd+"/testdata/pipeline1", tmpdir+"/pipeline1")
-	c.Assert(err, check.IsNil)
-	err = os.Symlink(cwd+"/testdata/pipeline1", tmpdir+"/pipeline1dup")
-	c.Assert(err, check.IsNil)
-
-	err = ioutil.WriteFile(tmpdir+"/chr1-12-100.bed", []byte("chr1\t12\t100\ttest.1\n"), 0644)
-	c.Check(err, check.IsNil)
-
-	c.Log("=== import testdata/ref ===")
-	exited := (&importer{}).RunCommand("import", []string{
-		"-local=true",
-		"-tag-library", "testdata/tags",
-		"-output-tiles",
-		"-save-incomplete-tiles",
-		"-o", tmpdir + "/lib1/library1.gob",
-		"testdata/ref.fasta",
-	}, nil, os.Stderr, os.Stderr)
-	c.Assert(exited, check.Equals, 0)
-
-	c.Log("=== import testdata/pipeline1 ===")
-	exited = (&importer{}).RunCommand("import", []string{
-		"-local=true",
-		"-tag-library", "testdata/tags",
-		"-output-tiles",
-		"-o", tmpdir + "/lib2/library2.gob",
-		tmpdir + "/pipeline1",
-	}, nil, os.Stderr, os.Stderr)
-	c.Assert(exited, check.Equals, 0)
-
-	c.Log("=== import pipeline1dup ===")
-	exited = (&importer{}).RunCommand("import", []string{
-		"-local=true",
-		"-tag-library", "testdata/tags",
-		"-output-tiles",
-		"-o", tmpdir + "/lib3/library3.gob",
-		tmpdir + "/pipeline1dup",
-	}, nil, os.Stderr, os.Stderr)
-	c.Assert(exited, check.Equals, 0)
-
-	slicedir := c.MkDir()
-
-	c.Log("=== slice ===")
-	exited = (&slicecmd{}).RunCommand("slice", []string{
-		"-local=true",
-		"-output-dir=" + slicedir,
-		"-tags-per-file=2",
-		tmpdir + "/lib1",
-		tmpdir + "/lib2",
-		tmpdir + "/lib3",
-	}, nil, os.Stderr, os.Stderr)
-	c.Check(exited, check.Equals, 0)
-	out, _ := exec.Command("find", slicedir, "-ls").CombinedOutput()
-	c.Logf("%s", out)
-
-	c.Log("=== dump ===")
-	{
-		dumpdir := c.MkDir()
-		exited = (&dump{}).RunCommand("dump", []string{
-			"-local=true",
-			"-tags=4,6,7",
-			"-input-dir=" + slicedir,
-			"-output-dir=" + dumpdir,
-		}, nil, os.Stderr, os.Stderr)
-		c.Check(exited, check.Equals, 0)
-		out, _ := exec.Command("find", dumpdir, "-ls").CombinedOutput()
-		c.Logf("%s", out)
-		dumped, err := ioutil.ReadFile(dumpdir + "/variants.csv")
-		c.Assert(err, check.IsNil)
-		c.Logf("%s", dumped)
-		c.Check("\n"+string(dumped), check.Matches, `(?ms).*\n6,1,1,chr2,349,AAAACTG.*`)
-	}
-
-	c.Log("=== slice-numpy ===")
-	{
-		npydir := c.MkDir()
-		exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
-			"-local=true",
-			"-input-dir=" + slicedir,
-			"-output-dir=" + npydir,
-		}, nil, os.Stderr, os.Stderr)
-		c.Check(exited, check.Equals, 0)
-		out, _ := exec.Command("find", npydir, "-ls").CombinedOutput()
-		c.Logf("%s", out)
-
-		f, err := os.Open(npydir + "/matrix.0000.npy")
-		c.Assert(err, check.IsNil)
-		defer f.Close()
-		npy, err := gonpy.NewReader(f)
-		c.Assert(err, check.IsNil)
-		c.Check(npy.Shape, check.DeepEquals, []int{4, 4})
-		variants, err := npy.GetInt16()
-		c.Check(variants, check.DeepEquals, []int16{2, 1, 1, 2, -1, -1, 1, 1, 2, 1, 1, 2, -1, -1, 1, 1})
-
-		annotations, err := ioutil.ReadFile(npydir + "/matrix.0000.annotations.csv")
-		c.Assert(err, check.IsNil)
-		c.Logf("%s", annotations)
-		for _, s := range []string{
-			"chr1:g.161A>T",
-			"chr1:g.178A>T",
-			"chr1:g.1_3delinsGGC",
-			"chr1:g.222_224del",
-		} {
-			c.Check(string(annotations), check.Matches, "(?ms).*"+s+".*")
-		}
-
-		annotations, err = ioutil.ReadFile(npydir + "/matrix.0002.annotations.csv")
-		c.Assert(err, check.IsNil)
-		c.Logf("%s", annotations)
-		for _, s := range []string{
-			",2,chr2:g.1_3delinsAAA",
-			",2,chr2:g.125_127delinsAAA",
-			",4,chr2:g.125_127delinsAAA",
-		} {
-			c.Check(string(annotations), check.Matches, "(?ms).*"+s+".*")
-		}
-	}
-
-	c.Log("=== slice-numpy + regions ===")
-	{
-		npydir := c.MkDir()
-		exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
-			"-local=true",
-			"-regions=" + tmpdir + "/chr1-12-100.bed",
-			"-input-dir=" + slicedir,
-			"-output-dir=" + npydir,
-			"-chunked-hgvs-matrix=true",
-		}, nil, os.Stderr, os.Stderr)
-		c.Check(exited, check.Equals, 0)
-		out, _ := exec.Command("find", npydir, "-ls").CombinedOutput()
-		c.Logf("%s", out)
-
-		f, err := os.Open(npydir + "/matrix.0000.npy")
-		c.Assert(err, check.IsNil)
-		defer f.Close()
-		npy, err := gonpy.NewReader(f)
-		c.Assert(err, check.IsNil)
-		c.Check(npy.Shape, check.DeepEquals, []int{4, 2})
-		variants, err := npy.GetInt16()
-		c.Check(variants, check.DeepEquals, []int16{2, 1, -1, -1, 2, 1, -1, -1})
-
-		annotations, err := ioutil.ReadFile(npydir + "/matrix.0000.annotations.csv")
-		c.Assert(err, check.IsNil)
-		c.Logf("%s", annotations)
-		for _, s := range []string{
-			"chr1:g.161A>T",
-			"chr1:g.178A>T",
-			"chr1:g.1_3delinsGGC",
-			"chr1:g.222_224del",
-		} {
-			c.Check(string(annotations), check.Matches, "(?ms).*"+s+".*")
-		}
-
-		for _, fnm := range []string{
-			npydir + "/matrix.0001.annotations.csv",
-			npydir + "/matrix.0002.annotations.csv",
-		} {
-			annotations, err := ioutil.ReadFile(fnm)
-			c.Assert(err, check.IsNil)
-			c.Check(string(annotations), check.Equals, "", check.Commentf(fnm))
-		}
-	}
-
-	err = ioutil.WriteFile(tmpdir+"/chr1and2-100-200.bed", []byte("chr1\t100\t200\ttest.1\nchr2\t100\t200\ttest.2\n"), 0644)
-	c.Check(err, check.IsNil)
-
-	c.Log("=== slice-numpy + regions + merge ===")
-	{
-		npydir := c.MkDir()
-		exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
-			"-local=true",
-			"-regions=" + tmpdir + "/chr1and2-100-200.bed",
-			"-input-dir=" + slicedir,
-			"-output-dir=" + npydir,
-			"-merge-output=true",
-			"-single-hgvs-matrix=true",
-		}, nil, os.Stderr, os.Stderr)
-		c.Check(exited, check.Equals, 0)
-		out, _ := exec.Command("find", npydir, "-ls").CombinedOutput()
-		c.Logf("%s", out)
-
-		f, err := os.Open(npydir + "/matrix.npy")
-		c.Assert(err, check.IsNil)
-		defer f.Close()
-		npy, err := gonpy.NewReader(f)
-		c.Assert(err, check.IsNil)
-		c.Check(npy.Shape, check.DeepEquals, []int{4, 4})
-		variants, err := npy.GetInt16()
-		if c.Check(err, check.IsNil) {
-			c.Check(variants, check.DeepEquals, []int16{
-				2, 1, 3, 1,
-				-1, -1, 4, 2,
-				2, 1, 3, 1,
-				-1, -1, 4, 2,
-			})
-		}
-
-		annotations, err := ioutil.ReadFile(npydir + "/matrix.annotations.csv")
-		c.Assert(err, check.IsNil)
-		c.Logf("%s", annotations)
-		for _, s := range []string{
-			"0,0,1,chr1:g.161A>T",
-			"0,0,1,chr1:g.178A>T",
-			"4,1,2,chr2:g.125_127delinsAAA",
-		} {
-			c.Check(string(annotations), check.Matches, "(?ms).*"+s+".*")
-		}
-	}
-
-	c.Log("=== slice-numpy + chunked hgvs matrix ===")
-	{
-		err = ioutil.WriteFile(tmpdir+"/casecontrol.tsv", []byte(`SampleID	CC
-pipeline1/input1	1
-pipeline1/input2	0
-pipeline1dup/input1	1
-pipeline1dup/input2	0
-`), 0600)
-		c.Assert(err, check.IsNil)
-		npydir := c.MkDir()
-		exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
-			"-local=true",
-			"-chunked-hgvs-matrix=true",
-			"-chi2-case-control-file=" + tmpdir + "/casecontrol.tsv",
-			"-chi2-case-control-column=CC",
-			"-chi2-p-value=0.5",
-			"-min-coverage=0.75",
-			"-input-dir=" + slicedir,
-			"-output-dir=" + npydir,
-		}, nil, os.Stderr, os.Stderr)
-		c.Check(exited, check.Equals, 0)
-		out, _ := exec.Command("find", npydir, "-ls").CombinedOutput()
-		c.Logf("%s", out)
-
-		annotations, err := ioutil.ReadFile(npydir + "/hgvs.chr2.annotations.csv")
-		c.Assert(err, check.IsNil)
-		c.Check(string(annotations), check.Equals, `0,chr2:g.1_3delinsAAA
-1,chr2:g.125_127delinsAAA
-2,chr2:g.241_245delinsAAAAA
-3,chr2:g.291C>A
-4,chr2:g.470_472del
-5,chr2:g.471G>A
-6,chr2:g.472G>A
-`)
-	}
-
-	c.Log("=== slice-numpy + onehotChunked ===")
-	{
-		err = ioutil.WriteFile(tmpdir+"/casecontrol.tsv", []byte(`SampleID	CC
-pipeline1/input1	1
-pipeline1/input2	0
-pipeline1dup/input1	1
-pipeline1dup/input2	0
-`), 0600)
-		c.Assert(err, check.IsNil)
-		npydir := c.MkDir()
-		exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
-			"-local=true",
-			"-chunked-onehot=true",
-			"-chi2-case-control-file=" + tmpdir + "/casecontrol.tsv",
-			"-chi2-case-control-column=CC",
-			"-chi2-p-value=0.5",
-			"-min-coverage=0.75",
-			"-input-dir=" + slicedir,
-			"-output-dir=" + npydir,
-		}, nil, os.Stderr, os.Stderr)
-		c.Check(exited, check.Equals, 0)
-		out, _ := exec.Command("find", npydir, "-ls").CombinedOutput()
-		c.Logf("%s", out)
-
-		f, err := os.Open(npydir + "/onehot.0002.npy")
-		c.Assert(err, check.IsNil)
-		defer f.Close()
-		npy, err := gonpy.NewReader(f)
-		c.Assert(err, check.IsNil)
-		c.Check(npy.Shape, check.DeepEquals, []int{4, 3})
-		onehot, err := npy.GetInt8()
-		if c.Check(err, check.IsNil) {
-			for r := 0; r < npy.Shape[0]; r++ {
-				c.Logf("%v", onehot[r*npy.Shape[1]:(r+1)*npy.Shape[1]])
-			}
-			c.Check(onehot, check.DeepEquals, []int8{
-				0, 1, 0, // input1
-				1, 0, 1, // input2
-				0, 1, 0, // dup/input1
-				1, 0, 1, // dup/input2
-			})
-		}
-	}
-
-	c.Log("=== slice-numpy + onehotSingle ===")
-	{
-		err = ioutil.WriteFile(tmpdir+"/casecontrol.tsv", []byte(`SampleID	CC
-pipeline1/input1	1
-pipeline1/input2	0
-pipeline1dup/input1	1
-pipeline1dup/input2	0
-`), 0600)
-		c.Assert(err, check.IsNil)
-		npydir := c.MkDir()
-		exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
-			"-local=true",
-			"-single-onehot=true",
-			"-chi2-case-control-file=" + tmpdir + "/casecontrol.tsv",
-			"-chi2-case-control-column=CC",
-			"-chi2-p-value=0.5",
-			"-min-coverage=0.75",
-			"-input-dir=" + slicedir,
-			"-output-dir=" + npydir,
-			"-debug-tag=1",
-		}, nil, os.Stderr, os.Stderr)
-		c.Check(exited, check.Equals, 0)
-		out, _ := exec.Command("find", npydir, "-ls").CombinedOutput()
-		c.Logf("%s", out)
-
-		f, err := os.Open(npydir + "/onehot.npy")
-		c.Assert(err, check.IsNil)
-		defer f.Close()
-		npy, err := gonpy.NewReader(f)
-		c.Assert(err, check.IsNil)
-		c.Check(npy.Shape, check.DeepEquals, []int{2, 12})
-		onehot, err := npy.GetUint32()
-		if c.Check(err, check.IsNil) {
-			for r := 0; r < npy.Shape[0]; r++ {
-				c.Logf("%v", onehot[r*npy.Shape[1]:(r+1)*npy.Shape[1]])
-			}
-			c.Check(onehot, check.DeepEquals, []uint32{
-				0, 2, 1, 3, 0, 2, 1, 3, 0, 2, 0, 2,
-				0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5,
-			})
-		}
-
-		f, err = os.Open(npydir + "/onehot-columns.npy")
-		c.Assert(err, check.IsNil)
-		defer f.Close()
-		npy, err = gonpy.NewReader(f)
-		c.Assert(err, check.IsNil)
-		c.Check(npy.Shape, check.DeepEquals, []int{5, 6})
-		onehotcols, err := npy.GetInt32()
-		if c.Check(err, check.IsNil) {
-			for r := 0; r < npy.Shape[0]; r++ {
-				c.Logf("%v", onehotcols[r*npy.Shape[1]:(r+1)*npy.Shape[1]])
-			}
-			c.Check(onehotcols, check.DeepEquals, []int32{
-				1, 4, 4, 4, 6, 6,
-				2, 2, 3, 4, 2, 3,
-				0, 0, 0, 0, 0, 0,
-				157299, 157299, 157299, 157299, 157299, 157299,
-				803273, 803273, 803273, 803273, 803273, 803273,
-			})
-		}
-	}
-}
-
-func (s *sliceSuite) TestSpanningTile(c *check.C) {
-	tmpdir := c.MkDir()
-	err := os.Mkdir(tmpdir+"/lib1", 0777)
-	c.Assert(err, check.IsNil)
-	err = os.Mkdir(tmpdir+"/lib2", 0777)
-	c.Assert(err, check.IsNil)
-	cwd, err := os.Getwd()
-	c.Assert(err, check.IsNil)
-	err = os.Symlink(cwd+"/testdata/pipeline1", tmpdir+"/pipeline1")
-	c.Assert(err, check.IsNil)
-	err = os.Symlink(cwd+"/testdata/pipeline1", tmpdir+"/pipeline1dup")
-	c.Assert(err, check.IsNil)
-
-	err = ioutil.WriteFile(tmpdir+"/chr1-12-100.bed", []byte("chr1\t12\t100\ttest.1\n"), 0644)
-	c.Check(err, check.IsNil)
-
-	c.Log("=== import testdata/ref ===")
-	exited := (&importer{}).RunCommand("import", []string{
-		"-local=true",
-		"-tag-library", "testdata/tags",
-		"-output-tiles",
-		"-save-incomplete-tiles",
-		"-o", tmpdir + "/lib1/library1.gob",
-		"testdata/ref.fasta",
-	}, nil, os.Stderr, os.Stderr)
-	c.Assert(exited, check.Equals, 0)
-
-	c.Log("=== import testdata/spanningtile ===")
-	exited = (&importer{}).RunCommand("import", []string{
-		"-local=true",
-		"-tag-library", "testdata/tags",
-		"-output-tiles",
-		"-o", tmpdir + "/lib2/library2.gob",
-		cwd + "/testdata/spanningtile",
-	}, nil, os.Stderr, os.Stderr)
-	c.Assert(exited, check.Equals, 0)
-
-	slicedir := c.MkDir()
-
-	c.Log("=== slice ===")
-	exited = (&slicecmd{}).RunCommand("slice", []string{
-		"-local=true",
-		"-output-dir=" + slicedir,
-		"-tags-per-file=2",
-		tmpdir + "/lib1",
-		tmpdir + "/lib2",
-	}, nil, os.Stderr, os.Stderr)
-	c.Check(exited, check.Equals, 0)
-	out, _ := exec.Command("find", slicedir, "-ls").CombinedOutput()
-	c.Logf("%s", out)
-
-	c.Log("=== dump ===")
-	{
-		dumpdir := c.MkDir()
-		exited = (&dump{}).RunCommand("dump", []string{
-			"-local=true",
-			"-tags=5,6",
-			"-input-dir=" + slicedir,
-			"-output-dir=" + dumpdir,
-		}, nil, os.Stderr, os.Stderr)
-		c.Check(exited, check.Equals, 0)
-		out, _ := exec.Command("find", dumpdir, "-ls").CombinedOutput()
-		c.Logf("%s", out)
-		dumped, err := ioutil.ReadFile(dumpdir + "/variants.csv")
-		c.Assert(err, check.IsNil)
-		c.Logf("%s", dumped)
-		// spanning tile for tag 5 with A>G snp in tag 6
-		c.Check("\n"+string(dumped), check.Matches, `(?ms).*\n5,2,0,chr2,225,.*AAAACTGATCCGAAAAAAATACAA.*`)
-		c.Check("\n"+string(dumped), check.Matches, `(?ms).*\n6,1,1,chr2,349,AAAACTGATCCAAAAAAAATACAA.*`)
-	}
-
-	c.Log("=== slice-numpy ===")
-	{
-		npydir := c.MkDir()
-		exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
-			"-local=true",
-			"-input-dir=" + slicedir,
-			"-output-dir=" + npydir,
-		}, nil, os.Stderr, os.Stderr)
-		c.Check(exited, check.Equals, 0)
-		out, _ := exec.Command("find", npydir, "-ls").CombinedOutput()
-		c.Logf("%s", out)
-
-		f, err := os.Open(npydir + "/matrix.0000.npy")
-		c.Assert(err, check.IsNil)
-		defer f.Close()
-		npy, err := gonpy.NewReader(f)
-		c.Assert(err, check.IsNil)
-		c.Check(npy.Shape, check.DeepEquals, []int{2, 4})
-		variants, err := npy.GetInt16()
-		c.Check(variants, check.DeepEquals, []int16{
-			-1, -1, 1, 1,
-			-1, -1, 1, 2,
-		})
-
-		annotations, err := ioutil.ReadFile(npydir + "/matrix.0000.annotations.csv")
-		c.Assert(err, check.IsNil)
-		c.Logf("%s", annotations)
-
-		f, err = os.Open(npydir + "/matrix.0002.npy")
-		c.Assert(err, check.IsNil)
-		defer f.Close()
-		npy, err = gonpy.NewReader(f)
-		c.Assert(err, check.IsNil)
-		c.Check(npy.Shape, check.DeepEquals, []int{2, 4})
-		variants, err = npy.GetInt16()
-		c.Check(variants, check.DeepEquals, []int16{
-			1, 1, 2, 1,
-			1, 1, 1, 1,
-		})
-
-		annotations, err = ioutil.ReadFile(npydir + "/matrix.0002.annotations.csv")
-		c.Assert(err, check.IsNil)
-		c.Logf("%s", annotations)
-		for _, s := range []string{
-			"chr2:g\\.360A>G",
-		} {
-			c.Check(string(annotations), check.Matches, "(?ms).*"+s+".*")
-		}
-	}
-
-	c.Log("=== slice-numpy + regions ===")
-	{
-		npydir := c.MkDir()
-		exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
-			"-local=true",
-			"-regions=" + tmpdir + "/chr1-12-100.bed",
-			"-input-dir=" + slicedir,
-			"-output-dir=" + npydir,
-			"-chunked-hgvs-matrix=true",
-		}, nil, os.Stderr, os.Stderr)
-		c.Check(exited, check.Equals, 0)
-		out, _ := exec.Command("find", npydir, "-ls").CombinedOutput()
-		c.Logf("%s", out)
-
-		f, err := os.Open(npydir + "/matrix.0000.npy")
-		c.Assert(err, check.IsNil)
-		defer f.Close()
-		npy, err := gonpy.NewReader(f)
-		c.Assert(err, check.IsNil)
-		c.Check(npy.Shape, check.DeepEquals, []int{2, 2})
-		variants, err := npy.GetInt16()
-		c.Check(variants, check.DeepEquals, []int16{-1, -1, -1, -1})
-
-		annotations, err := ioutil.ReadFile(npydir + "/matrix.0000.annotations.csv")
-		c.Assert(err, check.IsNil)
-		c.Check(string(annotations), check.Equals, "0,0,1,=,chr1,0,,,\n")
-
-		for _, fnm := range []string{
-			npydir + "/matrix.0001.annotations.csv",
-			npydir + "/matrix.0002.annotations.csv",
-		} {
-			annotations, err := ioutil.ReadFile(fnm)
-			c.Assert(err, check.IsNil)
-			c.Check(string(annotations), check.Equals, "", check.Commentf(fnm))
-		}
-	}
-
-	err = ioutil.WriteFile(tmpdir+"/chr1and2-100-200.bed", []byte("chr1\t100\t200\ttest.1\nchr2\t100\t200\ttest.2\n"), 0644)
-	c.Check(err, check.IsNil)
-
-	c.Log("=== slice-numpy + regions + merge ===")
-	{
-		npydir := c.MkDir()
-		exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
-			"-local=true",
-			"-regions=" + tmpdir + "/chr1and2-100-200.bed",
-			"-input-dir=" + slicedir,
-			"-output-dir=" + npydir,
-			"-merge-output=true",
-			"-single-hgvs-matrix=true",
-		}, nil, os.Stderr, os.Stderr)
-		c.Check(exited, check.Equals, 0)
-		out, _ := exec.Command("find", npydir, "-ls").CombinedOutput()
-		c.Logf("%s", out)
-
-		f, err := os.Open(npydir + "/matrix.npy")
-		c.Assert(err, check.IsNil)
-		defer f.Close()
-		npy, err := gonpy.NewReader(f)
-		c.Assert(err, check.IsNil)
-		c.Check(npy.Shape, check.DeepEquals, []int{2, 4})
-		variants, err := npy.GetInt16()
-		if c.Check(err, check.IsNil) {
-			c.Check(variants, check.DeepEquals, []int16{
-				-1, -1, 1, 1,
-				-1, -1, 1, 1,
-			})
-		}
-
-		annotations, err := ioutil.ReadFile(npydir + "/matrix.annotations.csv")
-		c.Assert(err, check.IsNil)
-		c.Check(string(annotations), check.Equals, "")
-	}
-
-	c.Log("=== slice-numpy + chunked hgvs matrix ===")
-	{
-		err = ioutil.WriteFile(tmpdir+"/casecontrol.tsv", []byte(`SampleID	CC
-spanningtile/input1	1
-`), 0600)
-		c.Assert(err, check.IsNil)
-		npydir := c.MkDir()
-		exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
-			"-local=true",
-			"-chunked-hgvs-matrix=true",
-			"-chi2-case-control-file=" + tmpdir + "/casecontrol.tsv",
-			"-chi2-case-control-column=CC",
-			"-chi2-p-value=1",
-			"-min-coverage=0.75",
-			"-input-dir=" + slicedir,
-			"-output-dir=" + npydir,
-		}, nil, os.Stderr, os.Stderr)
-		c.Check(exited, check.Equals, 0)
-		out, _ := exec.Command("find", npydir, "-ls").CombinedOutput()
-		c.Logf("%s", out)
-
-		annotations, err := ioutil.ReadFile(npydir + "/hgvs.chr2.annotations.csv")
-		c.Assert(err, check.IsNil)
-		c.Check(string(annotations), check.Equals, `0,chr2:g.360A>G
-`)
-	}
-
-	c.Log("=== slice-numpy + onehotChunked ===")
-	{
-		err = ioutil.WriteFile(tmpdir+"/casecontrol.tsv", []byte(`SampleID	CC
-spanningtile/input1	1
-`), 0600)
-		c.Assert(err, check.IsNil)
-		npydir := c.MkDir()
-		exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
-			"-local=true",
-			"-chunked-onehot=true",
-			"-chi2-case-control-file=" + tmpdir + "/casecontrol.tsv",
-			"-chi2-case-control-column=CC",
-			"-chi2-p-value=1",
-			"-min-coverage=0.75",
-			"-input-dir=" + slicedir,
-			"-output-dir=" + npydir,
-		}, nil, os.Stderr, os.Stderr)
-		c.Check(exited, check.Equals, 0)
-		out, _ := exec.Command("find", npydir, "-ls").CombinedOutput()
-		c.Logf("%s", out)
-
-		f, err := os.Open(npydir + "/onehot.0002.npy")
-		c.Assert(err, check.IsNil)
-		defer f.Close()
-		npy, err := gonpy.NewReader(f)
-		c.Assert(err, check.IsNil)
-		c.Check(npy.Shape, check.DeepEquals, []int{1, 2})
-		onehot, err := npy.GetInt8()
-		if c.Check(err, check.IsNil) {
-			for r := 0; r < npy.Shape[0]; r++ {
-				c.Logf("%v", onehot[r*npy.Shape[1]:(r+1)*npy.Shape[1]])
-			}
-			c.Check(onehot, check.DeepEquals, []int8{
-				0, 1, // input1
-			})
-		}
-	}
-
-	c.Log("=== slice-numpy + onehotSingle ===")
-	{
-		err = ioutil.WriteFile(tmpdir+"/casecontrol.tsv", []byte(`SampleID	CC
-spanningtile/input1	1
-`), 0600)
-		c.Assert(err, check.IsNil)
-		npydir := c.MkDir()
-		exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
-			"-local=true",
-			"-single-onehot=true",
-			"-chi2-case-control-file=" + tmpdir + "/casecontrol.tsv",
-			"-chi2-case-control-column=CC",
-			"-chi2-p-value=1",
-			"-min-coverage=0.75",
-			"-input-dir=" + slicedir,
-			"-output-dir=" + npydir,
-			"-debug-tag=1",
-		}, nil, os.Stderr, os.Stderr)
-		c.Check(exited, check.Equals, 0)
-		out, _ := exec.Command("find", npydir, "-ls").CombinedOutput()
-		c.Logf("%s", out)
-
-		f, err := os.Open(npydir + "/onehot.npy")
-		c.Assert(err, check.IsNil)
-		defer f.Close()
-		npy, err := gonpy.NewReader(f)
-		c.Assert(err, check.IsNil)
-		c.Check(npy.Shape, check.DeepEquals, []int{2, 1})
-		onehot, err := npy.GetUint32()
-		if c.Check(err, check.IsNil) {
-			for r := 0; r < npy.Shape[0]; r++ {
-				c.Logf("%v", onehot[r*npy.Shape[1]:(r+1)*npy.Shape[1]])
-			}
-			c.Check(onehot, check.DeepEquals, []uint32{0, 3})
-		}
-
-		f, err = os.Open(npydir + "/onehot-columns.npy")
-		c.Assert(err, check.IsNil)
-		defer f.Close()
-		npy, err = gonpy.NewReader(f)
-		c.Assert(err, check.IsNil)
-		c.Check(npy.Shape, check.DeepEquals, []int{5, 4})
-		onehotcols, err := npy.GetInt32()
-		if c.Check(err, check.IsNil) {
-			for r := 0; r < npy.Shape[0]; r++ {
-				c.Logf("%v", onehotcols[r*npy.Shape[1]:(r+1)*npy.Shape[1]])
-			}
-			c.Check(onehotcols, check.DeepEquals, []int32{
-				1, 1, 5, 5,
-				2, 2, 2, 2,
-				1, 0, 1, 0,
-				1000000, 1000000, 1000000, 1000000,
-				0, 0, 0, 0,
-			})
-		}
-	}
-}
-
-func (s *sliceSuite) Test_tv2homhet(c *check.C) {
-	cmd := &sliceNumpy{
-		cgnames:         []string{"sample1", "sample2", "sample3", "sample4"},
-		chi2Cases:       []bool{false, true, true, false},
-		chi2PValue:      .5,
-		includeVariant1: true,
-		minCoverage:     3,
-	}
-	cgs := map[string]CompactGenome{
-		"sample1": CompactGenome{
-			Variants: []tileVariantID{0, 0, 1, 1}, // hom tv=1
-		},
-		"sample2": CompactGenome{
-			Variants: []tileVariantID{0, 0, 5, 5}, // hom tv=2
-		},
-		"sample3": CompactGenome{
-			Variants: []tileVariantID{0, 0, 5, 1}, // het tv=1, tv=2
-		},
-		"sample4": CompactGenome{
-			Variants: []tileVariantID{0, 0, 9, 9}, // hom tv=3
-		},
-	}
-	maxv := tileVariantID(3)
-	remap := []tileVariantID{0, 1, 0, 0, 0, 2, 0, 0, 0, 3}
-	chunkstarttag := tagID(10)
-	fakevariant := TileVariant{Sequence: []byte("ACGT")}
-	seq := map[tagID][]TileVariant{}
-	for tag := tagID(10); tag < 12; tag++ {
-		seq[tag-chunkstarttag] = []TileVariant{TileVariant{}, fakevariant, TileVariant{}, TileVariant{}, TileVariant{}, fakevariant}
-		c.Logf("=== tag %d", tag)
-		chunk, xref := cmd.tv2homhet(cgs, maxv, remap, tag, chunkstarttag, seq)
-		c.Logf("chunk len=%d", len(chunk))
-		for _, x := range chunk {
-			c.Logf("%+v", x)
-		}
-		c.Logf("xref len=%d", len(xref))
-		for _, x := range xref {
-			c.Logf("%+v", x)
-		}
-		out := onehotcols2int8(chunk)
-		c.Logf("onehotcols2int8(chunk) len=%d", len(out))
-		for i := 0; i < len(out); i += len(chunk) {
-			c.Logf("%+v", out[i:i+len(chunk)])
-		}
-		coords := onehotChunk2Indirect(chunk)
-		c.Logf("onehotChunk2Indirect(chunk) len=%d", len(coords))
-		for _, x := range coords {
-			c.Logf("%+v", x)
-		}
-	}
-}