KCCG
diff --git a/‎src/__init__.py renamed to ‎mity/__init__.py b/‎src/__init__.py renamed to ‎mity/__init__.py
diff --git a/‎src/_version.py renamed to ‎mity/_version.py b/‎src/_version.py renamed to ‎mity/_version.py
diff --git a/‎res/annot/anticodon_positions.csv renamed to ‎mity/annot/anticodon_positions.csv b/‎res/annot/anticodon_positions.csv renamed to ‎mity/annot/anticodon_positions.csv
diff --git a/‎res/annot/gtf_annotations.csv renamed to ‎mity/annot/gtf_annotations.csv b/‎res/annot/gtf_annotations.csv renamed to ‎mity/annot/gtf_annotations.csv
diff --git a/‎res/annot/haplotype_data.csv renamed to ‎mity/annot/haplotype_data.csv b/‎res/annot/haplotype_data.csv renamed to ‎mity/annot/haplotype_data.csv
diff --git a/‎res/annot/mgrb_variants.csv renamed to ‎mity/annot/mgrb_variants.csv b/‎res/annot/mgrb_variants.csv renamed to ‎mity/annot/mgrb_variants.csv
diff --git a/‎res/annot/mito_dna_func_loc.csv renamed to ‎mity/annot/mito_dna_func_loc.csv b/‎res/annot/mito_dna_func_loc.csv renamed to ‎mity/annot/mito_dna_func_loc.csv
diff --git a/‎res/annot/mitomap_panel_annotations.csv renamed to ‎mity/annot/mitomap_panel_annotations.csv b/‎res/annot/mitomap_panel_annotations.csv renamed to ‎mity/annot/mitomap_panel_annotations.csv
diff --git a/‎res/annot/mitotip_score_fixed_del.csv renamed to ‎mity/annot/mitotip_score_fixed_del.csv b/‎res/annot/mitotip_score_fixed_del.csv renamed to ‎mity/annot/mitotip_score_fixed_del.csv
diff --git a/‎src/call.py renamed to ‎mity/call.py
Lines changed: 3 additions & 0 deletions b/‎src/call.py renamed to ‎mity/call.py
Lines changed: 3 additions & 0 deletions
@@ -3,9 +3,12 @@
 import subprocess
 import logging
 import os.path
+import configparser
 from .util import tabix, check_missing_file, create_prefix, bam_get_mt_contig, bam_has_RG
 from .normalise import do_normalise as vcfnorm
 
+config = configparser.ConfigParser()
+
 def do_call(bam_files, reference, genome=None, prefix=None, min_mq=30, min_bq=24,
             min_af=0.01, min_ac=4, p=0.002, normalise=True, 
             out_folder_path=".", region=None):