# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1366386545 18000
# Node ID 29b286896c500afb711c8a6f054cc7636abf6368
# Parent  cdbdac66d6b59037077e88aece171db7c4a324a1
Change the default number of Amino Acids to display after a missense to 10.

diff -r cdbdac66d6b5 -r 29b286896c50 snpEff_cds_report.py
--- a/snpEff_cds_report.py	Tue Mar 12 13:59:14 2013 -0400
+++ b/snpEff_cds_report.py	Fri Apr 19 10:49:05 2013 -0500
@@ -374,13 +374,14 @@
       return novel_peptide
     return None
   # [preAA,varAA,postAA, varPeptide, varOffset, subAA]
-  def getNonSynonymousPeptide(self,start_offset,end_offset,toStopCodon=True):
+  def getNonSynonymousPeptide(self,start_count,end_count,toStopCodon=True):
     (coding_seq, alt_seq, pos, coding_aa, var_aa, var_aa_pos, var_aa_end) = self.getSequences()
     if var_aa:
-      start_pos = max(var_aa_pos - start_offset,0) if start_offset and int(start_offset) >= 0 else 0
+      start_pos = max(var_aa_pos - start_count,0) if start_count and int(start_count) >= 0 else 0
       if toStopCodon:
         end_pos = var_aa_end
       else:
+        end_offset = end_count + 1
         end_pos = min(var_aa_pos+end_offset,len(var_aa)) if end_offset and int(end_offset) >= 0 else var_aa_end
       try:
         varAA = var_aa[var_aa_pos] if var_aa_pos < len(var_aa) else '_'