Merge pull request #250 from ncsa/misc-utils-splits-logic

Splits logic.

Author: keshav-gandhi

neat/read_simulator/utils/options.py

@@ -442,13 +442,15 @@ def log_configuration(self):
             _LOG.info(f'  - splitting input into size {self.parallel_block_size}')
         elif self.parallel_mode == 'contig':
             _LOG.info(f'Splitting input by contig.')
-        if not self.cleanup_splits or self.reuse_splits:
+        if self.reuse_splits:
             splits_dir = Path(f'{self.output_dir}/splits/')
-            if splits_dir.is_dir():
+            if not splits_dir.is_dir():
+                raise FileNotFoundError(f"reuse_splits=True but splits dir not found: {splits_dir}")
                 _LOG.info(f'Reusing existing splits {splits_dir}.')
-            else:
-                _LOG.warning(f'Reused splits set to True, but splits dir not found: {splits_dir}. Creating new splits')
-            _LOG.info(f'Preserving splits for next run in directory {self.splits_dir}.')
+                _LOG.info(f'Preserving splits for next run in directory {splits_dir}.')
+        elif not self.cleanup_splits:
+            splits_dir = Path(f'{self.output_dir}/splits/')
+            _LOG.info(f'Preserving splits for next run in directory {splits_dir}.')
         else:
             splits_dir = self.temp_dir_path / "splits"