limit scope of tests https://github.com/remiolsen/anglerfish/pull/85#…

…discussion_r1654331636

tests/test_anglerfish/test_demux/test_demux.py

@@ -88,6 +88,7 @@ def fixture():
 
 
 def test_run_minimap2(fixture):
+    """Check that the function runs successfully, not the output."""
     # Test alignment on single read
     to_test.run_minimap2(
         fastq_in=fixture["testdata_single"],
@@ -97,10 +98,6 @@ def test_run_minimap2(fixture):
         minimap_b=1,
     )
 
-    expected = "0ad8bdb6-e009-43c5-95b1-d381e699f983\t418\t302\t374\t+\ttruseq_i7\t67\t0\t67\t51\t64\t25\tNM:i:23\tms:i:275\tAS:i:266\tnn:i:10\ttp:A:P\tcm:i:5\ts1:i:29\ts2:i:0\tde:f:0.2388\trl:i:0\tcg:Z:11M2D33M7I21M\tcs:Z::11-ca:6*tg:13*nt*na*na*nc*nt*nt*ng*ng*nt*nc:1*ta:1+ctagaaa:2*gt*tg:17\n0ad8bdb6-e009-43c5-95b1-d381e699f983\t418\t45\t110\t+\ttruseq_i5\t58\t0\t58\t56\t66\t38\tNM:i:10\tms:i:313\tAS:i:305\tnn:i:0\ttp:A:P\tcm:i:10\ts1:i:37\ts2:i:0\tde:f:0.0667\trl:i:0\tcg:Z:15M1D6M7I3M1I33M\tcs:Z::15-a*cg:5+tcccgat:3+g:33\n"
-    received = open(fixture["paf_single"]).read()
-    assert expected == received
-
     # Create aligntment from multiple reads
     to_test.run_minimap2(
         fastq_in=fixture["testdata_multiple"],
@@ -118,28 +115,12 @@ def test_map_reads_to_alns(fixture):
         assert read_name == "0ad8bdb6-e009-43c5-95b1-d381e699f983"
         for aln in alns:
             if aln.adapter_name == "truseq_i7":
-                assert aln.read_name == "0ad8bdb6-e009-43c5-95b1-d381e699f983"
-                assert aln.adapter_name == "truseq_i7"
-                assert aln.read_len == 418
-                assert aln.read_start == 302
-                assert aln.read_end == 374
-                assert aln.read_strand == "+"
-                assert aln.cg == "cg:Z:11M2D33M7I21M"
                 assert (
                     aln.cs
                     == "cs:Z::11-ca:6*tg:13*nt*na*na*nc*nt*nt*ng*ng*nt*nc:1*ta:1+ctagaaa:2*gt*tg:17"
                 )
-                assert aln.q == 25
             else:
-                assert aln.read_name == "0ad8bdb6-e009-43c5-95b1-d381e699f983"
-                assert aln.adapter_name == "truseq_i5"
-                assert aln.read_len == 418
-                assert aln.read_start == 45
-                assert aln.read_end == 110
-                assert aln.read_strand == "+"
-                assert aln.cg == "cg:Z:15M1D6M7I3M1I33M"
                 assert aln.cs == "cs:Z::15-a*cg:5+tcccgat:3+g:33"
-                assert aln.q == 38
 
 
 def test_parse_cs(fixture):