Check sooner for HIV BLAST match, and fix low coverage check.

gene_splicer/outcome_summary.py

@@ -292,8 +292,7 @@ def reduce(self):
                         error_row['fail_rev_err_0'] in primer_errors):
                     self.data[sample]['error'] = self.errors.primer_error
                 # Case 6
-                elif (error_row['fail_fwd_err_0'] == self.errors.low_internal_cov or
-                      error_row['fail_rev_error_0'] == self.errors.low_internal_cov):
+                elif error_row['fail_error_0'] == self.errors.low_internal_cov:
                     self.data[sample]['error'] = self.errors.low_internal_cov
             else:
                 # Case 7, 8, 9

gene_splicer/primer_finder.py

@@ -179,6 +179,15 @@ def find_primers(
             contig_seq: str = row.get('contig') or row['sequence']
             contig_seq = contig_seq.upper()
 
+            if 'HIV' in seed_name:
+                non_hiv_rows = None
+            elif non_hiv_rows is not None:
+                new_row['error'] = errors.non_hiv
+                non_hiv_rows.append(new_row)
+                continue
+            else:
+                continue
+
             # If percent consensus cutoff is not max, skip
             if conseq_cutoff and conseq_cutoff != 'MAX':
                 new_row['error'] = errors.not_max
@@ -208,15 +217,6 @@ def find_primers(
             new_row['seqlen'] = len(contig_seq)
             new_row['sequence'] = contig_seq
 
-            if 'HIV' in seed_name:
-                non_hiv_rows = None
-            elif non_hiv_rows is not None:
-                new_row['error'] = errors.non_hiv
-                non_hiv_rows.append(new_row)
-                continue
-            else:
-                continue
-
             # Determine if sequence has non-tcga characters
             found_non_tcga = re.findall(non_tcga, contig_seq)
             mixtures = len([x for x in found_non_tcga if x[0].upper() != 'X'])