add simple test case for minimap2

tests/test_anglerfish/test_demux/test_demux.py

@@ -0,0 +1,30 @@
+import tempfile
+from pathlib import Path
+
+from anglerfish.demux import demux as to_test
+
+
+def test_run_minimap2():
+    tmp = tempfile.TemporaryDirectory()
+    tmp_path = Path(tmp.name)
+    paf_path = tmp_path / "test.paf"
+
+    to_test.run_minimap2(
+        fastq_in="testdata/explore/explore_testdata.fastq",
+        index_file="testdata/explore/illumina_ud.fasta",
+        output_paf=paf_path,
+        threads=1,
+        minimap_b=1,
+    )
+
+    expected = (
+        "\n".join(
+            [
+                "truseq_i5	58	0	58	+	truseq-read_10_C-index_5G	130	0	58	58	58	60	NM:i:0	ms:i:348	AS:i:348	nn:i:0	tp:A:P	cm:i:16	s1:i:54	s2:i:0	de:f:0	rl:i:0	cg:Z:58M	cs:Z::58",
+                "truseq_i7	57	0	57	+	truseq-read_10_C-index_5G	130	68	130	57	62	60	NM:i:5	ms:i:333	AS:i:328	nn:i:0	tp:A:P	cm:i:15	s1:i:54	s2:i:0	de:f:0.0172	rl:i:0	cg:Z:33M5D24M	cs:Z::33-ggggg:24",
+            ]
+        )
+        + "\n"
+    )
+
+    assert expected == open(paf_path).read()