update short read tools.

tools/metag_tools/blat_coverage_report.xml

@@ -58,14 +58,14 @@
 - The report showed overall coverage of reads on each chromosome location::
  
 	##title location ref.  cov.	A       T       C       G	
-	chr		614777	A		1	A(100)	T(0)	C(0)	G(0)
-	chr		614778	A		1	A(100)	T(0)	C(0)	G(0)
-	chr		614779	A		1	A(100)	T(0)	C(0)	G(0)
-	chr		614780	A		1	A(100)	T(0)	C(0)	G(0)
-	chr		614781	C		1	A(0)	T(0)	C(100)	G(0)
-	chr		614782	A		1	A(100)	T(0)	C(0)	G(0)
-	chr		614783	C		1	A(0)	T(0)	C(100)	G(0)
-	chr		614784	C		1	A(0)	T(0)	C(100)	G(0)
+	chr		614777	A	1	A(100)	T(0)	C(0)	G(0)
+	chr		614778	A	1	A(100)	T(0)	C(0)	G(0)
+	chr		614779	A	1	A(100)	T(0)	C(0)	G(0)
+	chr		614780	A	1	A(100)	T(0)	C(0)	G(0)
+	chr		614781	C	1	A(0)	T(0)	C(100)	G(0)
+	chr		614782	A	1	A(100)	T(0)	C(0)	G(0)
+	chr		614783	C	1	A(0)	T(0)	C(100)	G(0)
+	chr		614784	C	1	A(0)	T(0)	C(100)	G(0)
 	
 	Only show part of the result.
 	

tools/metag_tools/blat_wrapper.py

@@ -47,18 +47,21 @@ def __main__():
     output_file = sys.argv[4]
     
     try:
-        min_iden = float(sys.argv[5])
+        test = float(sys.argv[5])
+        min_iden = sys.argv[5]
     except:
         stop_err('Invalid value for minimal identity')
     
-    try:    
-        tile_size = int(sys.argv[6])
-        assert tile_size >= 6 and tile_size <= 18
+    try:  
+        test = int(sys.argv[6])
+        tile_size = sys.argv[6]
+        assert test >= 6 and test <= 18
     except:
         stop_err('Invalid value for tile size. DNA word size must be between 6 and 18.')
         
     try:
-        one_off = int(sys.argv[7])
+        test = int(sys.argv[7])
+        one_off = sys.argv[7]
     except:
         stop_err('Invalid value for mismatch numbers in the word')
         

tools/metag_tools/megablast_wrapper.py

@@ -22,16 +22,19 @@ def __main__():
     
     # megablast parameters
     try:
-        mega_word_size = int(sys.argv[4])        # -W
+        test = int(sys.argv[4])
+        mega_word_size = sys.argv[4]        # -W
     except:
         stop_err('Invalid value for word size')
     
-    try:    
-        mega_iden_cutoff = float(sys.argv[5])      # -p
+    try:
+        test = float(sys.argv[5])
+        mega_iden_cutoff = sys.argv[5]      # -p
     except:
         stop_err('Invalid value for identity cut-off')
     
     try:
+        test = int(sys.argv[6])
         mega_disc_word = sys.argv[6]        # -t
     except:
         stop_err('Invalid value for discontiguous word template')