Troubleshoot

Author: standage

microhapulator/tests/test_pipe.py

@@ -67,9 +67,11 @@ def test_pipe_gbr_usc10(tmp_path):
     args = microhapulator.cli.get_parser().parse_args(arglist)
     microhapulator.cli.pipe.main(args)
     expected = SimulatedProfile(fromfile=data_file("prof/gbr-usc10-sim.json"))
+    print("DEBUGger", *list((tmp_path / "analysis" / "gbr-usc" / "03typing").glob("*")), sep="\n")
     observed = TypingResult(
         fromfile=tmp_path / "analysis" / "gbr-usc" / "03typing" / "gbr-usc-type.json"
     )
+    assert False
     diff = list(mhapi.diff(observed, expected))
     assert len(diff) == 0
     report = tmp_path / "report" / "report.html"

microhapulator/workflows/preproc-paired.smk

@@ -72,7 +72,6 @@ rule filter_ambiguous:
         ambig_thresh=config["ambiguous_thresh"],
         out_prefix="analysis/{sample}/01preprocessing/{sample}",
     run:
-        print("DEBUG", wildcards.sample, input)
         ambig_filter = AmbigPairedReadFilter(*input, params.out_prefix, params.ambig_thresh)
         ambig_filter.filter()
         with open(output.counts, "w") as fh: