Add --no-max-contig-length option to turn off splitting on --max-contig-length

Author: jgrg

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "tola-agp-tpf-utils"
-version = "1.3.1"
+version = "1.3.2"
 readme = "README.md"
 requires-python = ">=3.11"
 dependencies = [

src/tola/assembly/build_assembly.py

@@ -302,7 +302,13 @@ def __build_name_and_sort_assemblies(
                 new_asm = Assembly(self.name, curated=curated)
                 assemblies[asm_key] = new_asm
 
-            for cut_scffld in self.cut_scaffold_if_too_long(scffld):
+            cut_scaffolds: list[Scaffold]
+            if self.max_contig_length is not None:
+                cut_scaffolds = self.cut_scaffold_if_too_long(scffld)
+            else:
+                cut_scaffolds = [scffld]
+
+            for cut_scffld in cut_scaffolds:
                 new_asm.add_scaffold(cut_scffld)
 
                 if cut_scffld.rank == 1:

src/tola/assembly/scripts/pretext_to_asm.py

@@ -199,6 +199,12 @@ def ul(txt):
         """,
     default=2_000_000_000,
 )
+@click.option(
+    "--no-max-contig-length",
+    flag_value=True,
+    default=False,
+    help="Turns off splitting on --max-contig-length",
+)
 def cli(
     assembly_file: Path,
     pretext_file: Path,
@@ -210,6 +216,7 @@ def cli(
     keep_map_order: bool,
     default_asm_name: str,
     max_contig_length: int,
+    no_max_contig_length: bool,
 ):
     logfile = setup_logging(log_level, output_file, write_log, clobber)
 
@@ -230,7 +237,7 @@ def cli(
     build_asm = BuildAssembly(
         "stdout",
         autosome_prefix=autosome_prefix,
-        max_contig_length=max_contig_length,
+        max_contig_length=None if no_max_contig_length else max_contig_length,
     )
     build_asm.remap_to_input_assembly(prtxt_asm, input_asm)