Parallelization renaming in the utils folder scripts.

neat/read_simulator/utils/options.py

@@ -439,7 +439,7 @@ def log_configuration(self):
 
         if self.parallel_mode == 'size':
             _LOG.info(f'Splitting reference into chunks.')
-            _LOG.info(f'  - splitting input into size {self.size}')
+            _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:

neat/read_simulator/utils/split_inputs.py

@@ -67,15 +67,15 @@ def main(options: Options, reference_index: dict) -> tuple[dict, int]:
     # We'll keep track of chunks by contig, to help us out later
     split_fasta_dict: dict[str, dict[tuple[int, int], Path]] = {key: {} for key in reference_index.keys()}
     for contig, seq_record in reference_index.items():
-        if options.mode == "contig":
+        if options.parallel_mode == "contig":
             stem = f"{idx:0{pad}d}__{contig}"
             fa = options.splits_dir / f"{stem}.fa.gz"
             write_fasta(contig, seq_record.seq.upper(), fa)
             split_fasta_dict[contig][(0, len(seq_record))] = fa
             idx += 1
             written += 1
         else:
-            for start, subseq in chunk_record(seq_record.seq.upper(), options.size, overlap):
+            for start, subseq in chunk_record(seq_record.seq.upper(), options.parallel_block_size, overlap):
                 stem = f"{idx:0{pad}d}__{contig}"
                 fa = options.splits_dir / f"{stem}.fa.gz"
                 write_fasta(contig, subseq, fa)