# HG changeset patch
# User pjbriggs
# Date 1460454656 14400
# Node ID 85dee233e0f348cbf11341234305c4a75a2b5ef3
# Parent  c6d5ddf728c37b5a0f7c94bd5d0ac54e2e9970ce
Bug fix to pal_filter.py.

diff -r c6d5ddf728c3 -r 85dee233e0f3 pal_filter.py
--- a/pal_filter.py	Mon Mar 21 06:47:23 2016 -0400
+++ b/pal_filter.py	Tue Apr 12 05:50:56 2016 -0400
@@ -456,8 +456,10 @@
 
                 # check that both primer sequences can be seen in the
                 # assembled contig
-                if y or ReverseComplement1(y) in assembly_no_id and z or \
-                                    ReverseComplement1(z) in assembly_no_id:
+                if ((y in assembly_no_id) or \
+                    (ReverseComplement1(y) in assembly_no_id)) and \
+                    ((z in assembly_no_id) or \
+                    (ReverseComplement1(z) in assembly_no_id)):
                     if y in assembly_no_id:
                         # get the positions of the primers in the assembly
                         # (can be used to predict fragment length)