Added stopiferrors option python part of metaDMG

src/metaDMG/cli/cli.py

@@ -132,6 +132,14 @@ def create_config(
         rich_help_panel="LCA parameters",
     ),
     # GENERAL PARAMETERS
+    stopIfErrors: Optional[int] = typer.Option(
+        0,
+        "-stopIfErrors",
+        "-Z",
+        help="Temporary hack to bypass sorting check if SO tag does not exist in sam header. Values 0 or 1. zero=dont check",
+        callback=lambda x: cli_utils.is_positive_int_or_None(x),
+        rich_help_panel="General parameters",
+    ),
     metaDMG_cpp: str = typer.Option(
         "./metaDMG-cpp",
         "--metaDMG-cpp",
@@ -276,6 +284,7 @@ def create_config(
         sample_suffix=sample_suffix,
         long_name=long_name,
         damage_mode=damage_mode,
+        stopIfErrors=stopIfErrors,
         __version__=__version__,
     )
 

src/metaDMG/cli/cli_utils.py

@@ -459,6 +459,7 @@ def get_config_dict(
     sample_prefix: str = "",
     sample_suffix: str = "",
     long_name: bool = False,
+    stopIfErrors: int = 1,
     damage_mode: DAMAGE_MODE = DAMAGE_MODE.LCA,
     __version__: str = "",
 ) -> dict:
@@ -486,6 +487,7 @@ def get_config_dict(
             "weight_type": weight_type,
             "custom_database": custom_database,
             "forward_only": forward_only,
+            "stopIfErrors": stopIfErrors,
             #
             "output_dir": output_dir,
             "parallel_samples": parallel_samples,

src/metaDMG/fit/serial.py

@@ -91,6 +91,7 @@ def get_LCA_command(config: Config) -> str:
         f"-weighttype {config['weight_type']} "
         f"-fix_ncbi {config['custom_database']} "
         f"-tempfolder {config['path_tmp']}/ "
+        f"-stopIfErrors {config['stopIfErrors']} "
     )
     return command[:-1]
 
@@ -145,6 +146,7 @@ def get_damage_command(config: Config) -> str:
         f"--runmode {runmode} "
         f"--outname {outname} "
         f"{config['bam']} "
+        f"-stopIfErrors {config['stopIfErrors']} "
     )
     return command[:-1]
 

src/metaDMG/utils.py

@@ -170,6 +170,7 @@ def make_configs(
     d.setdefault("cores_per_sample", 1)
     d.setdefault("damage_mode", "lca")
     d.setdefault("min_reads", 0)
+    d.setdefault("stopIfErrors", 1)
     d["force"] = force
 
     paths = ["names", "nodes", "acc2tax", "output_dir", "config_file"]