regex sequence now ensured to be uppercase

Author: xsitarcik

src/schemas/locus.py

@@ -37,13 +37,13 @@ def __init__(
             self.flank_length = flank_length
 
         if sequence:
-            self.sequence = sequence
+            self.sequence = sequence.upper()
             self.noting = noting
 
         else:
             seq, noting = self.prepare_sequence(main_config.reference_path)
             self.noting = noting
-            self.sequence = seq
+            self.sequence = seq.upper()
 
     def prepare_sequence(self, reference_path: str):
         fa_seq: str = pysam.faidx(reference_path, self.coord)

src/squiggler/Squiggler.py

@@ -72,4 +72,4 @@ def _save_all(self, output_path: str, sequences: Tuple[str, str, str, str, str,
         with open(fasta_path, 'w') as file:
             file.write('type,sequence\n')
             for idx, i in enumerate(tmpl.LOCUS_NAMES):
-                file.write(i+','+sequences[idx]+'\n')
+                file.write(i+','+sequences[idx].upper()+'\n')