--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snp-filter.py	Wed Jan 24 14:18:21 2018 -0500
@@ -0,0 +1,27 @@
+from Bio import SeqIO
+import vcf
+
+
+import argparse
+import os
+import sys
+
+def passes(vcf_feature, contigs, edge_length=500, window_size=1000, max_snps=3):
+	return True
+
+def main(input_vcf, input_reference, output_included, output_excluded=os.devnull, *args, **kwargs)
+	contigs = list(SeqIO.parse(input_reference, 'fasta'))
+	included = vcf.Writer(output_included)
+	excluded = vcf.Writer(output_excluded)
+	for feature in vcf.Reader(input_vcf):
+		if passes(feature, contigs, *args, **kwargs):
+			included.write(feature)
+		else:
+			excluded.write(feature)
+
+if __name__ == '__main__':
+	parser = argparse.ArgumentParser()
+	parser.add_argument('input_vcf', type=argparse.FileType())
+	parser.add_argument('input_reference', type=argparse.FileType())
+	parser.add_argument('output_included', type=argparse.FileType('w'))
+	parser.add_argument('--excluded', '-x', dest='output_excluded', type=argparse.FileType('w'), default=os.devnull)
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