diff --git a/MACS2/cPeakDetect.pyx b/MACS2/cPeakDetect.pyx
index 982f5464..5db777f4 100644
--- a/MACS2/cPeakDetect.pyx
+++ b/MACS2/cPeakDetect.pyx
@@ -1,4 +1,4 @@
-# Time-stamp: <2014-08-22 13:49:38 Tao Liu>
+# Time-stamp: <2014-10-23 15:18:38 Tao Liu>
 
 """Module Description
 
@@ -337,8 +337,7 @@ class PeakDetect:
                                                 save_SPMR = self.opt.do_SPMR,
                                                 cutoff_analysis_filename = self.opt.cutoff_analysis_file )
 
-        # calculate pvalue scores
-        if self.opt.trackline: self.scoretrack.enable_trackline()
+        if self.opt.trackline: scorecalculator.enable_trackline()
 
         # call peaks
         call_summits = self.opt.call_summits
diff --git a/setup.py b/setup.py
index a6cb5530..23600774 100644
--- a/setup.py
+++ b/setup.py
@@ -1,5 +1,5 @@
 #!/usr/bin/env python
-# Time-stamp: <2014-10-23 15:06:57 Tao Liu>
+# Time-stamp: <2014-10-23 15:48:18 Tao Liu>
 
 """Description
 
@@ -37,23 +37,22 @@ def main():
         sys.stderr.write("CRITICAL: Python version must be 2.7!\n")
         sys.exit(1)
 
-    ext_modules = [Extension("MACS2.cProb", ["MACS2/cProb.c"], libraries=["m"], include_dirs=numpy_include_dir ),
-                   Extension("MACS2.IO.cParser",["MACS2/IO/cParser.c"], include_dirs=numpy_include_dir),
-                   Extension("MACS2.cPileup", ["MACS2/cPileup.c"], include_dirs=numpy_include_dir ),
-                   Extension("MACS2.cArray", ["MACS2/cArray.c"]),                       
-                   Extension("MACS2.cPeakModel", ["MACS2/cPeakModel.c"], include_dirs=numpy_include_dir),                   
-                   Extension("MACS2.cPeakDetect", ["MACS2/cPeakDetect.c"]),
-                   Extension("MACS2.cSignal", ["MACS2/cSignal.c"], include_dirs=numpy_include_dir),
-                   Extension("MACS2.IO.cPeakIO", ["MACS2/IO/cPeakIO.c"],),
-                   Extension("MACS2.IO.cBedGraphIO", ["MACS2/IO/cBedGraphIO.c"],),                   
-                   Extension("MACS2.IO.cFixWidthTrack", ["MACS2/IO/cFixWidthTrack.c"], include_dirs=numpy_include_dir),
-                   Extension("MACS2.IO.cPairedEndTrack", ["MACS2/IO/cPairedEndTrack.c"], include_dirs=numpy_include_dir),
-                   Extension("MACS2.IO.cBedGraph", ["MACS2/IO/cBedGraph.c"], libraries=["m"]),
-                   Extension("MACS2.IO.cScoreTrack", ["MACS2/IO/cScoreTrack.c"], include_dirs=numpy_include_dir ),
-                   #Extension("MACS2.IO.cDiffScore", ["MACS2/IO/cDiffScore.c"], include_dirs=numpy_include_dir ),                   
-                   Extension("MACS2.IO.cCallPeakUnit", ["MACS2/IO/cCallPeakUnit.c"], include_dirs=numpy_include_dir),
-                   Extension("MACS2.hashtable", ["MACS2/hashtable.c"], include_dirs=["MACS2/",numpy_get_include()]),
-                   Extension("MACS2.Statistics", ["MACS2/Statistics.c", "MACS2/cStatistics.c"], libraries=["m"], include_dirs=["MACS2/",numpy_get_include()]),
+    ext_modules = [Extension("MACS2.cProb", ["MACS2/cProb.c"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
+                   Extension("MACS2.IO.cParser",["MACS2/IO/cParser.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
+                   Extension("MACS2.cPileup", ["MACS2/cPileup.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
+                   Extension("MACS2.cArray", ["MACS2/cArray.c"], extra_compile_args=["-w","-Ofast"]),                       
+                   Extension("MACS2.cPeakModel", ["MACS2/cPeakModel.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
+                   Extension("MACS2.cPeakDetect", ["MACS2/cPeakDetect.c"], extra_compile_args=["-w","-Ofast"]),
+                   Extension("MACS2.cSignal", ["MACS2/cSignal.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
+                   Extension("MACS2.IO.cPeakIO", ["MACS2/IO/cPeakIO.c"], extra_compile_args=["-w","-Ofast"]),
+                   Extension("MACS2.IO.cBedGraphIO", ["MACS2/IO/cBedGraphIO.c"], extra_compile_args=["-w","-Ofast"]),                   
+                   Extension("MACS2.IO.cFixWidthTrack", ["MACS2/IO/cFixWidthTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
+                   Extension("MACS2.IO.cPairedEndTrack", ["MACS2/IO/cPairedEndTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
+                   Extension("MACS2.IO.cBedGraph", ["MACS2/IO/cBedGraph.c"], libraries=["m"], extra_compile_args=["-w","-Ofast"]),
+                   Extension("MACS2.IO.cScoreTrack", ["MACS2/IO/cScoreTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
+                   Extension("MACS2.IO.cCallPeakUnit", ["MACS2/IO/cCallPeakUnit.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
+                   Extension("MACS2.hashtable", ["MACS2/hashtable.c"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=["-w","-Ofast"]),
+                   Extension("MACS2.Statistics", ["MACS2/Statistics.c", "MACS2/cStatistics.c"], libraries=["m"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=["-w","-Ofast"]),
                    ]
     
     setup(name="MACS2",
diff --git a/setup_w_cython.py b/setup_w_cython.py
index feb48a94..0457c34f 100644
--- a/setup_w_cython.py
+++ b/setup_w_cython.py
@@ -1,5 +1,5 @@
 #!/usr/bin/env python
-# Time-stamp: <2014-10-23 15:07:06 Tao Liu>
+# Time-stamp: <2014-10-23 15:48:33 Tao Liu>
 
 """Description: 
 
@@ -45,42 +45,40 @@ def main():
         sys.exit(1)
 
     if has_cython:
-        ext_modules = [Extension("MACS2.cProb", ["MACS2/cProb.pyx"], libraries=["m"], include_dirs=numpy_include_dir ),
-                       Extension("MACS2.IO.cParser",["MACS2/IO/cParser.pyx"], include_dirs=numpy_include_dir),
-                       Extension("MACS2.cPileup", ["MACS2/cPileup.pyx"], include_dirs=numpy_include_dir ),
-                       Extension("MACS2.cArray", ["MACS2/cArray.pyx"]),                       
-                       Extension("MACS2.cPeakModel", ["MACS2/cPeakModel.pyx"], include_dirs=numpy_include_dir),                   
-                       Extension("MACS2.cPeakDetect", ["MACS2/cPeakDetect.pyx"]),
-                       Extension("MACS2.cSignal", ["MACS2/cSignal.pyx"], include_dirs=numpy_include_dir),
-                       Extension("MACS2.IO.cPeakIO", ["MACS2/IO/cPeakIO.pyx"],),
-                       Extension("MACS2.IO.cBedGraphIO", ["MACS2/IO/cBedGraphIO.pyx"],),                   
-                       Extension("MACS2.IO.cFixWidthTrack", ["MACS2/IO/cFixWidthTrack.pyx"], include_dirs=numpy_include_dir),
-                       Extension("MACS2.IO.cPairedEndTrack", ["MACS2/IO/cPairedEndTrack.pyx"], include_dirs=numpy_include_dir),
-                       Extension("MACS2.IO.cBedGraph", ["MACS2/IO/cBedGraph.pyx"], libraries=["m"]),
-                       Extension("MACS2.IO.cScoreTrack", ["MACS2/IO/cScoreTrack.pyx"], include_dirs=numpy_include_dir ), 
-                       #Extension("MACS2.IO.cDiffScore", ["MACS2/IO/cDiffScore.pyx"], include_dirs=numpy_include_dir ),                      
-                       Extension("MACS2.IO.cCallPeakUnit", ["MACS2/IO/cCallPeakUnit.pyx"], include_dirs=numpy_include_dir),
-                       Extension("MACS2.hashtable", ["MACS2/hashtable.pyx"], include_dirs=["MACS2/",numpy_get_include()]),
-                       Extension("MACS2.Statistics", ["MACS2/Statistics.pyx", "MACS2/cStatistics.c"], libraries=["m"], include_dirs=["MACS2/",numpy_get_include()]),
+        ext_modules = [Extension("MACS2.cProb", ["MACS2/cProb.pyx"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
+                       Extension("MACS2.IO.cParser",["MACS2/IO/cParser.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
+                       Extension("MACS2.cPileup", ["MACS2/cPileup.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
+                       Extension("MACS2.cArray", ["MACS2/cArray.pyx"], extra_compile_args=["-w","-Ofast"]),                       
+                       Extension("MACS2.cPeakModel", ["MACS2/cPeakModel.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
+                       Extension("MACS2.cPeakDetect", ["MACS2/cPeakDetect.pyx"], extra_compile_args=["-w","-Ofast"]),
+                       Extension("MACS2.cSignal", ["MACS2/cSignal.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
+                       Extension("MACS2.IO.cPeakIO", ["MACS2/IO/cPeakIO.pyx"], extra_compile_args=["-w","-Ofast"]),
+                       Extension("MACS2.IO.cBedGraphIO", ["MACS2/IO/cBedGraphIO.pyx"], extra_compile_args=["-w","-Ofast"]),                   
+                       Extension("MACS2.IO.cFixWidthTrack", ["MACS2/IO/cFixWidthTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
+                       Extension("MACS2.IO.cPairedEndTrack", ["MACS2/IO/cPairedEndTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
+                       Extension("MACS2.IO.cBedGraph", ["MACS2/IO/cBedGraph.pyx"], libraries=["m"], extra_compile_args=["-w","-Ofast"]),
+                       Extension("MACS2.IO.cScoreTrack", ["MACS2/IO/cScoreTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
+                       Extension("MACS2.IO.cCallPeakUnit", ["MACS2/IO/cCallPeakUnit.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
+                       Extension("MACS2.hashtable", ["MACS2/hashtable.pyx"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=["-w","-Ofast"]),
+                       Extension("MACS2.Statistics", ["MACS2/Statistics.pyx", "MACS2/cStatistics.c"], libraries=["m"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=["-w","-Ofast"]),
                        ]
     else:
-        ext_modules = [Extension("MACS2.cProb", ["MACS2/cProb.c"], libraries=["m"], include_dirs=numpy_include_dir ),
-                       Extension("MACS2.IO.cParser",["MACS2/IO/cParser.c"], include_dirs=numpy_include_dir),
-                       Extension("MACS2.cPileup", ["MACS2/cPileup.c"], include_dirs=numpy_include_dir),
-                       Extension("MACS2.cSignal", ["MACS2/cSignal.c"], include_dirs=numpy_include_dir),
-                       Extension("MACS2.cArray", ["MACS2/cArray.c"]),                                              
-                       Extension("MACS2.cPeakModel", ["MACS2/cPeakModel.c"], include_dirs=numpy_include_dir),                   
-                       Extension("MACS2.cPeakDetect", ["MACS2/cPeakDetect.c"]),
-                       Extension("MACS2.IO.cPeakIO", ["MACS2/IO/cPeakIO.c"],),
-                       Extension("MACS2.IO.cBedGraphIO", ["MACS2/IO/cBedGraphIO.c"],),                   
-                       Extension("MACS2.IO.cFixWidthTrack", ["MACS2/IO/cFixWidthTrack.c"], include_dirs=numpy_include_dir),
-                       Extension("MACS2.IO.cPairedEndTrack", ["MACS2/IO/cPairedEndTrack.c"], include_dirs=numpy_include_dir),
-                       Extension("MACS2.IO.cBedGraph", ["MACS2/IO/cBedGraph.c"], libraries=["m"]),
-                       Extension("MACS2.IO.cScoreTrack", ["MACS2/IO/cScoreTrack.c"], include_dirs=numpy_include_dir),
-                       #Extension("MACS2.IO.cDiffScore", ["MACS2/IO/cDiffScore.c"], include_dirs=numpy_include_dir ),                       
-                       Extension("MACS2.IO.cCallPeakUnit", ["MACS2/IO/cCallPeakUnit.c"], include_dirs=numpy_include_dir),
-                       Extension("MACS2.hashtable", ["MACS2/hashtable.c"], include_dirs=["MACS2/",numpy_get_include()]),
-                       Extension("MACS2.Statistics", ["MACS2/Statistics.c", "MACS2/cStatistics.c"], libraries=["m"], include_dirs=["MACS2/",numpy_get_include()]),
+        ext_modules = [Extension("MACS2.cProb", ["MACS2/cProb.c"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
+                       Extension("MACS2.IO.cParser",["MACS2/IO/cParser.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
+                       Extension("MACS2.cPileup", ["MACS2/cPileup.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
+                       Extension("MACS2.cArray", ["MACS2/cArray.c"], extra_compile_args=["-w","-Ofast"]),                       
+                       Extension("MACS2.cPeakModel", ["MACS2/cPeakModel.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
+                       Extension("MACS2.cPeakDetect", ["MACS2/cPeakDetect.c"], extra_compile_args=["-w","-Ofast"]),
+                       Extension("MACS2.cSignal", ["MACS2/cSignal.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
+                       Extension("MACS2.IO.cPeakIO", ["MACS2/IO/cPeakIO.c"], extra_compile_args=["-w","-Ofast"]),
+                       Extension("MACS2.IO.cBedGraphIO", ["MACS2/IO/cBedGraphIO.c"], extra_compile_args=["-w","-Ofast"]),                   
+                       Extension("MACS2.IO.cFixWidthTrack", ["MACS2/IO/cFixWidthTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
+                       Extension("MACS2.IO.cPairedEndTrack", ["MACS2/IO/cPairedEndTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
+                       Extension("MACS2.IO.cBedGraph", ["MACS2/IO/cBedGraph.c"], libraries=["m"], extra_compile_args=["-w","-Ofast"]),
+                       Extension("MACS2.IO.cScoreTrack", ["MACS2/IO/cScoreTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
+                       Extension("MACS2.IO.cCallPeakUnit", ["MACS2/IO/cCallPeakUnit.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
+                       Extension("MACS2.hashtable", ["MACS2/hashtable.c"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=["-w","-Ofast"]),
+                       Extension("MACS2.Statistics", ["MACS2/Statistics.c", "MACS2/cStatistics.c"], libraries=["m"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=["-w","-Ofast"]),
                        ]
 
     setup(name="MACS2",