2015.4.20 release

ChangeLog

@@ -1,11 +1,14 @@
-2015-03-16  Tao Liu  <[email protected]>
-	MACS version 2.1.0 20150316 (tag:rc)
+2015-04-20  Tao Liu  <[email protected]>
+	MACS version 2.1.0 20150420 (tag:rc)
 
 	* New commands
 
-	1) bdgopt ... 
+	1) bdgopt: some convenient functions to modify bedGraph files.
 
-	2) cmbreps ...
+	2) cmbreps: Combine scores from two replicates. Including three
+	methods: 1. take the maximum; 2. take the average; 3. use Fisher's
+	method to combine two p-value scores. After that, user can use
+	bdgpeakcall to call peaks on combined scores.
 
 	* New features
 

MACS2/Constants.py

@@ -1,4 +1,4 @@
-MACS_VERSION = "2.1.0.20150316"
+MACS_VERSION = "2.1.0.20150420"
 #MACSDIFF_VERSION = "1.0.4 20110212 (tag:alpha)"
 FILTERDUP_VERSION = "1.0.0 20140616"
 RANDSAMPLE_VERSION = "1.0.0 20120703"

MACS2/Pileup.pyx

@@ -1,4 +1,4 @@
-# Time-stamp: <2015-04-20 14:15:35 Tao Liu>
+# Time-stamp: <2015-04-20 14:26:53 Tao Liu>
 
 """Module Description: For pileup functions.
 
@@ -689,7 +689,7 @@ cpdef quick_pileup ( np.ndarray[np.int32_t, ndim=1] start_poss, np.ndarray[np.in
         int32_t * end_poss_ptr
         int32_t * ret_p_ptr     # pointer for position array 
         float32_t * ret_v_ptr     # pointer for value array
-        int max_pileup = 0
+        #int max_pileup = 0
 
     start_poss_ptr = <int32_t *> start_poss.data
     end_poss_ptr = <int32_t *> end_poss.data
@@ -731,8 +731,8 @@ cpdef quick_pileup ( np.ndarray[np.int32_t, ndim=1] start_poss, np.ndarray[np.in
                 I += 1
                 pre_p = p
             pileup += 1
-            if pileup > max_pileup:
-                max_pileup = pileup
+            #if pileup > max_pileup:
+            #    max_pileup = pileup
             i_s += 1
             start_poss_ptr += 1
         elif start_poss_ptr[0] > end_poss_ptr[0]:

setup.py

@@ -1,5 +1,5 @@
 #!/usr/bin/env python
-# Time-stamp: <2015-03-12 00:17:23 Tao Liu>
+# Time-stamp: <2015-04-20 14:32:39 Tao Liu>
 
 """Description
 
@@ -55,7 +55,7 @@ def main():
                    ]
 
     setup(name="MACS2",
-          version="2.1.0.20150316",
+          version="2.1.0.20150420",
           description="Model Based Analysis for ChIP-Seq data",
           author='Tao Liu',
           author_email='[email protected]',

setup_w_cython.py

@@ -1,5 +1,5 @@
 #!/usr/bin/env python
-# Time-stamp: <2015-03-12 00:17:39 Tao Liu>
+# Time-stamp: <2015-04-20 14:32:32 Tao Liu>
 
 """Description: 
 
@@ -80,7 +80,7 @@ def main():
                        ]
 
     setup(name="MACS2",
-          version="2.1.0.20150316",
+          version="2.1.0.20150420",
           description="Model Based Analysis for ChIP-Seq data",
           author='Tao Liu',
           author_email='[email protected]',