Addressing review comments

cubi_tk/snappy/common.py

@@ -16,18 +16,6 @@ class CouldNotFindBioMedSheet(Exception):
     """Raised when BioMedSheet could not be found in configuration file."""
 
 
-def load_snappy_config(path_yaml):
-    """Load SNAPPY configuration file.
-
-    :param path_yaml: Path to SNAPPY configuration file.
-    :type path_yaml: pathlib.Path
-
-    :return: Returns configuration dictionary.
-    """
-    with open(path_yaml, "rt") as f:
-        return yaml.safe_load(f)
-
-
 def load_sheet_tsv(path_tsv, tsv_shortcut="germline"):
     """Load sample sheet.
 

cubi_tk/snappy/itransfer_sv_calling.py

@@ -5,6 +5,7 @@
 import typing
 
 from logzero import logger
+import yaml
 
 from . import common
 from .itransfer_common import IndexLibrariesOnlyMixin, SnappyItransferCommandBase
@@ -15,7 +16,7 @@
 
 class SnappyStepNotFoundException(Exception):
     def __str__(self):
-        return "snappy-pipeline is not installed. This function will not work."
+        return "snappy-pipeline config does not define the expected steps this function needs."
 
 
 class SnappyItransferSvCallingCommand(IndexLibrariesOnlyMixin, SnappyItransferCommandBase):
@@ -30,7 +31,8 @@ def __init__(self, args):
         super().__init__(args)
 
         path = common.find_snappy_root_dir(self.args.base_path or os.getcwd())
-        config = common.load_snappy_config(path / ".snappy_pipeline/config.yaml")
+        with open(str(path / ".snappy_pipeline/config.yaml", "rt")) as f:
+            config = yaml.safe_load(f)
         self.step_name = None
         for step_name in self.__class__.step_names:
             if not self.step_name and step_name in config["step_config"]: