A new version of ngsfilger without a bug about error count between primers and sequence

src/ngsfilter.py

@@ -356,6 +356,7 @@ def annotate(sequence,options):
         sequence['tail_quality']=q
         
     primers = options.primers
+    if options.debug:
         print >>sys.stderr,"directmatch"
     directmatch = [(p,p(sequence)) for p in primers]
     
@@ -363,6 +364,7 @@ def annotate(sequence,options):
     directmatch.sort(cmp=sortMatch)
     directmatch=directmatch[0] if directmatch[0][1] is not None else None
     
+    if options.debug:
         print  >>sys.stderr,">>>>",directmatch
     if directmatch is None:
         sequence['error']='No primer match'
@@ -389,11 +391,13 @@ def annotate(sequence,options):
     del sequence['cut']
     
     primers = options.primers[directmatch[0]]
+    if options.debug:
         print  >>sys.stderr,"reverse match"
     reversematch = [(p,p(sequence)) for p in primers if p is not None]
     reversematch.sort(cmp=sortMatch)
     reversematch = reversematch[0] if reversematch[0][1] is not None else None
     
+    if options.debug:
         print  >>sys.stderr,"<<<<",reversematch
     if reversematch is None and None not in primers:
         if directmatch[0].direct: