removed debug data dumping

Author: Vinzenz

src/svirlpool/scripts/align_consensus_to_reference.py

@@ -15,6 +15,7 @@
 
 from . import util
 
+
 # %%
 # =============================================================================
 # cut alignments at given reference positions

src/svirlpool/scripts/consensus_align_lib.py

@@ -323,9 +323,6 @@ def save_merge_svs_in_dict_alignments_input(input, path: Path | str):
     log.info(f"Saved input for merge_svs_in_dict_alignments to {path}")
 
 
-
-
-
 # --- horizontal merge --- #
 # test this!
 def merge_svs_in_dict_alignments(

src/svirlpool/scripts/consensus_legacy.py

@@ -1262,7 +1262,6 @@ def create_read_partitions_with_initial_signal_clusters(
     return all_dict_partitions, all_alignment_paths
 
 
-
 # %%
 # =============================================================================
 

src/svirlpool/scripts/filter_nonseparated.py

@@ -199,6 +199,7 @@ def process_func(args):
 
 # %%
 
+
 def filter_nonseparated(
     path_bam: Path,
     out_path: Path,

src/svirlpool/scripts/filter_signaldepths.py

@@ -15,7 +15,6 @@
 from . import util
 
 
-
 # %%
 def filter_signaldepths(
     path_signaldepths, path_sampledicts, max_median_coverage_factor, output_path

src/svirlpool/scripts/nonunique_regions.py

@@ -11,6 +11,7 @@
 
 # %%
 
+
 def check_if_all_chromosomes_are_in_refdict(
     path_mappability: Path, path_reference: Path
 ):

src/svirlpool/scripts/stratify_signals_DELs.py

@@ -8,7 +8,6 @@
 # from . import alignments_to_rafs
 
 
-
 # def split_DELs(
 #         path_signaldepths: Path,
 #         path_output: Path,

src/svirlpool/scripts/unique_regions.py

@@ -53,7 +53,6 @@ def merge_bedfiles_and_subtract_from_reference(
         p5.communicate()
 
 
-
 def create_unique_regions_bed_file(
     paths_bedfiles: list[Path], reference: Path, output: Path, min_size: int
 ) -> None:

src/svirlpool/scripts/util.py

@@ -2056,7 +2056,6 @@ def cut_alignments_in_regions(
     return None
 
 
-
 def insert_table_metadata(path_database: str, table_name: str, tag: str):
     """
     Inserts metadata for a table into a hardcoded metadata table in the SQLite database.

src/svirlpool/scripts/vcf_to_bed.py

@@ -6,6 +6,7 @@
 
 import vcfpy
 
+
 def vcf_deletions_to_bed(path_vcf: Path, path_bed: Path, min_size: int):
     reader = vcfpy.Reader.from_path(path_vcf)
     with open(path_bed, "w") as f: