replicate RuntimeError in test_outputvcf

tests/data/var_greater.bkp → tests/data/var_greater.bp

@@ -1,12 +1,12 @@
 Sample_1_1
 YRI	1	59423086	85.107755
-CEU	1	2147483647	266.495714
+CEU	1	248924793	286.279234
 Sample_1_2
 YRI	1	59423086	85.107755
-YRI	1	2147483647	266.495714
+YRI	1	248924793	286.279234
 Sample_2_1
 CEU	1	59423086	85.107755
-YRI	1	2147483647	266.495714
+YRI	1	248924793	286.279234
 Sample_2_2
 CEU	1	59423086	85.107755
-CEU	1	2147483647	266.495714
+CEU	1	248924793	286.279234

tests/data/var_greater.vcf

@@ -4,4 +4,4 @@
 ##contig=<ID=chr1>
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00096	HG00097	HG00099	HG00100	HG00101
 chr1	10114	chr1:10114:T:C	T	C	.	.	.	GT	1|1	1|1	0|0	0|0	0|0
-chr1	249403765	chr1:249403765:A:G	A	G	.	.	.	GT	0|0	0|0	1|1	1|1	1|1
+chr1	248924809	chr1:248924809:A:G	A	G	.	.	.	GT	0|0	0|0	1|1	1|0	1|1

tests/test_outputvcf.py

@@ -112,11 +112,11 @@ def test_end_bkp_coords():
 
 def test_variants_greater_than_last_coord():
     log = getLogger(name="test")
-    bkp_file = DATADIR / "var_greater.bkp"
-    vcf_file = DATADIR / "var_greater.vcf.gz"
+    bkp_file = DATADIR / "var_greater.bp"
+    vcf_file = DATADIR / "var_greater.vcf"
     model_file = DATADIR / "outvcf_gen.dat"
     sampleinfo_file = DATADIR / "outvcf_info.tab"
-    out_file = DATADIR / "outvcf_out.vcf.gz"
+    out_file = DATADIR / "outvcf_out.pgen"
     chroms = ["1"]
     bkps = _get_breakpoints(bkp_file, model_file)
 
@@ -135,26 +135,22 @@ def test_variants_greater_than_last_coord():
         log,
     )
 
-    # read in vcf file
-    vcf = VCF(str(out_file))
+    # read in pgen file
+    vcf = GenotypesPLINK(out_file, log=log)
     for var in vcf:
-        if var.CHROM == "chr1" and var.POS == 10114:
-            assert var.genotypes[0] == [0, 0, True]
-            assert var.format("POP")[0] == "YRI,YRI"
-            assert var.genotypes[1] == [1, 1, True]
-            assert var.format("POP")[1] == "CEU,CEU"
-
-        elif var.CHROM == "chr1" and var.POS == 249403765:
-            assert var.genotypes[0] == [0, 1, True]
-            assert var.format("POP")[0] == "CEU,YRI"
-            assert var.genotypes[1] == [1, 0, True]
-            assert var.format("POP")[1] == "YRI,CEU"
-
+        if var.variants["chrom"] == "chr1" and var.variants["pos"] == 10114:
+            np.testing.assert_allclose(var.data[0], [0, 0, 1])
+            np.testing.assert_allclose(var.data[1], [1, 1, 1])
+        elif var.variants["chrom"] == "chr1" and var.variants["pos"] == 248924809:
+            np.testing.assert_allclose(var.data[0], [0, 1, 1])
+            np.testing.assert_allclose(var.data[1], [1, 0, 1])
         else:
             assert False
 
     # Clean up by removing the output file from output_vcf
     out_file.unlink()
+    out_file.with_suffix(".pvar").unlink()
+    out_file.with_suffix(".psam").unlink()
 
 
 def test_alt_chrom_name():