Merge branch 'hotfix/1.0.1'

carjed · Jul 23, 2018 · 0b25d98 · 0b25d98
2 parents 08a69eb + f09b75a
commit 0b25d98
Showing 1 changed file with 5 additions and 5 deletions.
diff --git a/util.py b/util.py
@@ -271,18 +271,18 @@ def processVCF(args, inputvcf, subtypes_dict, par):
 
     for record in vcf_reader:
 
-        # Filter by allele count
-        if (record.INFO['AC'] > args.maxac > 0):
-            numsites_skip += 1
-            continue
-
         # Filter by SNP status, # alt alleles, and FILTER column
         if (not record.is_snp or 
             len(record.ALT) != 1 or 
             record.FILTER is not None):
             numsites_skip += 1
             continue
 
+        # Filter by allele count
+        if (record.INFO['AC'] > args.maxac > 0):
+            numsites_skip += 1
+            continue
+
         # check and update chromosome sequence
         if record.CHROM != chrseq:
             sequence = fasta_reader[record.CHROM]