Merge branch 'main' into 144-break-uprecombine-larger-genomes

Author: joshfactorial

neat/read_simulator/utils/generate_variants.py

@@ -205,7 +205,12 @@ def generate_variants(
                 if location == 0:
                     continue
                 trinuc = reference[location: location+3].seq.upper()
-                if "N" in trinuc:
+                disallowed_chars = False
+                for letter in trinuc:
+                    if letter not in ALLOWED_NUCL:
+                        disallowed_chars = True
+                        break
+                if disallowed_chars:
                     continue
                 temp_variant = mutation_model.generate_snv(trinuc, location, options.rng)
 

neat/read_simulator/utils/read.py

@@ -406,8 +406,8 @@ def align_seqs(self):
         cig_length = 0
         curr_char = ''
         cig_string = ''
-        # Find first match
-        for char in range(len(self.read_sequence)):
+        # Find first match. Added a +1 because all my matches were coming up short.
+        for char in range(len(self.read_sequence) + 1):
             if aligned_template_seq[char] == '-':  # insertion
                 if curr_char == 'I':  # more insertions
                     cig_count += 1