Add test for variant at right end of spanning tile.

refs #19271

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

diff --git a/slice_test.go b/slice_test.go
index b61ba18eebfd97000a2c8be384cd0aff9ce760d4..ec879589954eb5f9e04c38a0fc0805c0b88fb6e5 100644 (file)
--- a/slice_test.go
+++ b/slice_test.go
@@ -446,7 +446,7 @@ func (s *sliceSuite) TestSpanningTile(c *check.C) {
                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).*\n5,1,0,chr2,225,.*AAAACTGATCCGAAAAAAATACAA.*`)
+               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.*`)
        }
 
@@ -467,9 +467,12 @@ func (s *sliceSuite) TestSpanningTile(c *check.C) {
                defer f.Close()
                npy, err := gonpy.NewReader(f)
                c.Assert(err, check.IsNil)
-               c.Check(npy.Shape, check.DeepEquals, []int{1, 4})
+               c.Check(npy.Shape, check.DeepEquals, []int{2, 4})
                variants, err := npy.GetInt16()
-               c.Check(variants, check.DeepEquals, []int16{-1, -1, 1, 1})
+               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)
@@ -480,9 +483,12 @@ func (s *sliceSuite) TestSpanningTile(c *check.C) {
                defer f.Close()
                npy, err = gonpy.NewReader(f)
                c.Assert(err, check.IsNil)
-               c.Check(npy.Shape, check.DeepEquals, []int{1, 4})
+               c.Check(npy.Shape, check.DeepEquals, []int{2, 4})
                variants, err = npy.GetInt16()
-               c.Check(variants, check.DeepEquals, []int16{1, 1, 1, 2})
+               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)
@@ -513,9 +519,9 @@ func (s *sliceSuite) TestSpanningTile(c *check.C) {
                defer f.Close()
                npy, err := gonpy.NewReader(f)
                c.Assert(err, check.IsNil)
-               c.Check(npy.Shape, check.DeepEquals, []int{1, 2})
+               c.Check(npy.Shape, check.DeepEquals, []int{2, 2})
                variants, err := npy.GetInt16()
-               c.Check(variants, check.DeepEquals, []int16{-1, -1})
+               c.Check(variants, check.DeepEquals, []int16{-1, -1, -1, -1})
 
                annotations, err := ioutil.ReadFile(npydir + "/matrix.0000.annotations.csv")
                c.Assert(err, check.IsNil)
@@ -554,11 +560,12 @@ func (s *sliceSuite) TestSpanningTile(c *check.C) {
                defer f.Close()
                npy, err := gonpy.NewReader(f)
                c.Assert(err, check.IsNil)
-               c.Check(npy.Shape, check.DeepEquals, []int{1, 4})
+               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,
                        })
                }
 
@@ -665,9 +672,7 @@ spanningtile/input1 1
                        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, 1,
-                       })
+                       c.Check(onehot, check.DeepEquals, []uint32{0, 3})
                }
 
                f, err = os.Open(npydir + "/onehot-columns.npy")
@@ -675,18 +680,18 @@ spanningtile/input1       1
                defer f.Close()
                npy, err = gonpy.NewReader(f)
                c.Assert(err, check.IsNil)
-               c.Check(npy.Shape, check.DeepEquals, []int{5, 2})
+               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{
-                               5, 5,
-                               2, 2,
-                               1, 0,
-                               1000000, 1000000,
-                               0, 0,
+                               1, 1, 5, 5,
+                               2, 2, 2, 2,
+                               1, 0, 1, 0,
+                               1000000, 1000000, 1000000, 1000000,
+                               0, 0, 0, 0,
                        })
                }
        }

diff --git a/testdata/spanningtile/input2.1.fasta b/testdata/spanningtile/input2.1.fasta
new file mode 100644 (file)
index 0000000..8bd6142
--- /dev/null
+++ b/testdata/spanningtile/input2.1.fasta
@@ -0,0 +1,20 @@
+>chr1
+nnngtctacctcgagaagccccgacctctgaataagatctttgaacatctcaagggattgtgtatcttgttgggtgtacgcgcgccagcccgcagcatta
+ggagaactgtgctccgccttcaga
+ccccttgggtaaaatgccgcgcaatatgttgattacacttgctgcccatctgaaaggtcgccttatcaatcctatgctgaatgccctctaaggagttcca
+acacatgctagcgcgtcggggtgg
+tcgccgcatgggacatgttggggtcccgtagctccggtcgatgtaggcacgcgttttgccgaggagatagatcatcagctgacctatagattcgtctgtc
+gactctagcagagtggccagccac
+aaggtttatattcagtcgaaatggacgggtcccgaacttgcacggacctaacgggactcgcctttcgtaataaccgaacctctaggccgccgcgagatca
+cctcccgagccgagccacccgtca
+tgatagccatcccgcacctagcgcacggaacttcgaccgatcccatattaacgtgtctcttatcctcccgctactgcgtgccttgccactcgtttactat
+>chr2
+tttttatagcagtagcggttgcgataatgcgcactaaggtggccataacttagccacacagactgcgacctcggtgtcaatctttaggcgatgactagtg
+gttattaataataacttatcatca
+cttccggggaaactagcgtaaaaaccgccgtcgcagtataccaccttatacctgtgccactcaatacaggagttgctcagcccaagacaccaacgactaa
+gctctcaaaccttgtatttttctt
+atgtcctcgcttggattatggggactcgcagtaaatgacaaccgtgcccgctggccctggccggaccgcgcgtccgtaagtagcgatcgagtcctgcagt
+aaaactgatccaaaaaaaatacaa
+acaccacgtttataccctgttgagtcgccacgtaacgtattaacgtatgaacggcccggttttcttatctcgcaccgctagtttgccctggcggtcgtgg
+cctatgagtcaatcctattttcaa
+gatgagtatgtataaggcggcctgtcacgtgaaacctaggatacccaggtacctagggtcatttgctccccgttccccgcggcggacatccgaatatatc

diff --git a/testdata/spanningtile/input2.2.fasta b/testdata/spanningtile/input2.2.fasta
new file mode 100644 (file)
index 0000000..0af9db3
--- /dev/null
+++ b/testdata/spanningtile/input2.2.fasta
@@ -0,0 +1,20 @@
+>chr1
+nnngtctacctcgagaagccccgacctctgaataagatctttgaacatctcaagggattgtgtatcttgttgggtgtacgcgcgccagcccgcagcatta
+ggagaactgtgctccgccttcaga
+ccccttgggtaaaatgccgcgcaatatgttgattacacttgctgcccatctgaaaggtcgccttatcaatcctatgctgaatgccctctaaggagttcca
+acacatgctagcgcgtcggggtgg
+tcgccgcatgggacatgttggggtcccgtagctccggtcgatgtaggcacgcgttttgccgaggagatagatcatcagctgacctatagattcgtctgtc
+
+aaggtttatattcagtcgaaatggacgggtcccgaacttgcacggacctaacgggactcgGGtttcgtaataaccgaacctctaggccgccgcgagatca
+cctcccgagccgagccacccgtca
+tgatagccatcccgcacctagcgcacggaacttcgaccgatcccatattaacgtgtctcttatcctcccgctactgcgtgccttgccactcgtttactat
+>chr2
+tttttatagcagtagcggttgcgataatgcgcactaaggtggccataacttagccacacagactgcgacctcggtgtcaatctttaggcgatgactagtg
+gttattaataataacttatcatca
+cttccggggaaactagcgtaaaaaccgccgtcgcagtataccaccttatacctgtgccactcaatacaggagttgctcagcccaagacaccaacgactaa
+gctctcaaaccttgtatttttctt
+atgtcctcgcttggattatggggactcgcagtaaatgacaaccgtgcccgctggccctggccggaccgcgcgtccgtaagtagcgatcgagtcctgcagt
+aaaactgatccaaaaaaaatacaa
+acaccacgtttataccctgttgagtcgccacgtaacgtattaacgtatgaacggcccggttttcttatctcgcaccgctagtttgccctggcggtcgtgg
+cctatgagtcaatcctattttcaa
+gatgagtatgtataaggcggcctgtcacgtgaaacctaggatacccaggtacctagggtcatttgctccccgttccccgcggcggacatccgaatatatc