1) Fixed issue macs3-project#76: information about broad cutoff and n…

…arrow cutoff will

be correctly displayed in the output xls file.
2) Remove a 'print' line for debug.

MACS2/IO/CallPeakUnit.pyx

@@ -1,4 +1,4 @@
-# Time-stamp: <2015-04-20 14:21:12 Tao Liu>
+# Time-stamp: <2015-04-24 10:05:31 Tao Liu>
 
 """Module for Calculate Scores.
 
@@ -216,6 +216,7 @@ cdef float mean_from_value_length ( np.ndarray value, list length ):
         int32_t tmp_l
         float tmp_v, sum_v
 
+    sum_v = 0
     tmp = zip( value, length )
     l = sum( length )
 
@@ -256,7 +257,7 @@ cdef tuple find_optimal_cutoff( list x, list y ):
         sst = sum( ( npy[:i] - np.mean( npy[:i] ) ) ** 2 )
         sse = sum( ( npy[:i] - m*npx[:i] - c ) ** 2 )
         rsq = 1 - sse/sst
-        print i, x[i], y[i], m, c, rsq
+        #print i, x[i], y[i], m, c, rsq
     return ( 1.0, 1.0 )
 
 

MACS2/OptValidator.py

@@ -1,4 +1,4 @@
-# Time-stamp: <2015-03-05 13:56:30 Tao Liu>
+# Time-stamp: <2015-04-24 17:17:25 Tao Liu>
 
 """Module Description
 
@@ -173,10 +173,19 @@ def opt_validate ( options ):
         ))
 
     if options.pvalue:
-        options.argtxt +=  "# pvalue cutoff = %.2e\n" % (options.pvalue)
-        options.argtxt +=  "# qvalue will not be calculated and reported as -1 in the final output.\n"
+        if options.broad:
+            options.argtxt +=  "# pvalue cutoff for narrow/strong regions = %.2e\n" % (options.pvalue)
+            options.argtxt +=  "# pvalue cutoff for broad/weak regions = %.2e\n" % (options.broadcutoff)
+            options.argtxt +=  "# qvalue will not be calculated and reported as -1 in the final output.\n"
+        else:
+            options.argtxt +=  "# pvalue cutoff = %.2e\n" % (options.pvalue)
+            options.argtxt +=  "# qvalue will not be calculated and reported as -1 in the final output.\n"
     else:
-        options.argtxt +=  "# qvalue cutoff = %.2e\n" % (options.qvalue)
+        if options.broad:
+            options.argtxt +=  "# qvalue cutoff for narrow/strong regions = %.2e\n" % (options.qvalue)
+            options.argtxt +=  "# qvalue cutoff for broad/weak regions = %.2e\n" % (options.broadcutoff)
+        else:
+            options.argtxt +=  "# qvalue cutoff = %.2e\n" % (options.qvalue)
 
     if options.downsample:
         options.argtxt += "# Larger dataset will be randomly sampled towards smaller dataset.\n"