initial work on an extensible VCF filter

setup.py

@@ -10,11 +10,16 @@
 
 setup(
     name='PyVCF',
-    py_modules=['vcf'],
-    scripts=['vcf_melt'],
+    py_modules=['vcf', 'vcf_filter'],
+    scripts=['vcf_melt', 'vcf_filter.py'],
     author='James Casbon',
     author_email='[email protected]',
     description='Variant Call Format (VCF) parser for python',
     test_suite='test.test_vcf.suite',
-    requires=requires
+    requires=requires,
+    entry_points = {
+        'vcf.filters': [
+            'site_quality = vcf_filter:SiteQuality',
+        ]
+    }
 )

test/example.vcf

@@ -18,7 +18,7 @@
 ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
 20	14370	rs6054257	G	A	29	PASS	NS=3;DP=14;AF=0.5;DB;H2	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:.,.
-20	17330	.	T	A	3	q10	NS=3;DP=11;AF=0.017	GT:GQ:DP:HQ	0|0:49:3:58,50	0|1:3:5:65,3	0/0:41:3
-20	1110696	rs6040355	A	G,T	67	PASS	NS=2;DP=10;AF=0.333,0.667;AA=T;DB	GT:GQ:DP:HQ	1|2:21:6:23,27	2|1:2:0:18,2	2/2:35:4
-20	1230237	.	T	.	47	PASS	NS=3;DP=13;AA=T	GT:GQ:DP:HQ	0|0:54:7:56,60	0|0:48:4:51,51	0/0:61:2
-20	1234567	microsat1	GTCT	G,GTACT	50	PASS	NS=3;DP=9;AA=G	GT:GQ:DP	./.:35:4	0/2:17:2	1/1:40:3
+20	17330	.	T	A	3	q10	NS=3;DP=11;AF=0.017	GT:GQ:DP:HQ	0|0:49:3:58,50	0|1:3:5:65,3	0/0:41:3:65,3
+20	1110696	rs6040355	A	G,T	67	PASS	NS=2;DP=10;AF=0.333,0.667;AA=T;DB	GT:GQ:DP:HQ	1|2:21:6:23,27	2|1:2:0:18,2	2/2:35:4:65,4
+20	1230237	.	T	.	47	PASS	NS=3;DP=13;AA=T	GT:GQ:DP:HQ	0|0:54:7:56,60	0|0:48:4:51,51	0/0:61:2:65,3
+20	1234567	microsat1	GTCT	G,GTACT	50	PASS	NS=3;DP=9;AA=G	GT:GQ:DP	./.:35:4	0/2:17:2	1/1:40:3:65,3

vcf.py

@@ -237,7 +237,7 @@ def add_format(self, fmt):
         self.FORMAT = self.FORMAT + ':' + fmt
 
     def add_filter(self, flt):
-        if self.FILTER == '.':
+        if self.FILTER == '.' or self.FILTER == 'PASS':
             self.FILTER = ''
         else:
             self.FILTER = self.FILTER + ';'