From 2f230a0d189beb147fc39b475a25e36fd9b1de5e Mon Sep 17 00:00:00 2001
From: Kanwei Li <kanwei@gmail.com>
Date: Tue, 26 Oct 2010 13:46:03 -0400
Subject: [PATCH] Fix solid_qual_stats tool when value is 0 or not a valid int.
 Fixes #405

---
 tools/solid_tools/solid_qual_stats.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tools/solid_tools/solid_qual_stats.py b/tools/solid_tools/solid_qual_stats.py
index c5ab0d5aba9..53744ea34bd 100644
--- a/tools/solid_tools/solid_qual_stats.py
+++ b/tools/solid_tools/solid_qual_stats.py
@@ -31,6 +31,7 @@ def __main__():
         infile_name = infile_score_name
     
     readlen = None
+    invalid_lines = 0
     j = 0
     for line in file( infile_name ):
         line = line.strip()
@@ -39,18 +40,17 @@ def __main__():
         elems = line.split()
         try:
             for item in elems:
-                assert int(item)
-            if not(readlen):
+                int(item)
+            if not readlen:
                 readlen = len(elems)
             if len(elems) != readlen:
                 print "Note: Reads in the input dataset are of variable lengths."
             j += 1
-        except:
+        except ValueError:
             invalid_lines += 1
         if j > 10:
             break
         
-    invalid_lines = 0
     position_dict = {}
     print >>fout, "column\tcount\tmin\tmax\tsum\tmean\tQ1\tmed\tQ3\tIQR\tlW\trW"
     for k,line in enumerate(file( infile_name )):
@@ -132,7 +132,7 @@ def __main__():
     if invalid_lines:
         print "Skipped %d reads as invalid." %invalid_lines
     if invalid_positions:
-        print "Skipped stats computation for %d read postions." %invalid_positions
+        print "Skipped stats computation for %d read positions." %invalid_positions
         
 if __name__=="__main__":
     __main__()