Merge pull request #446 from macs3-project/fix/macs3/peakmodel442

Fix: 0 pair for paired-peak model #442

ChangeLog

@@ -1,5 +1,5 @@
-2020-12-08  Tao Liu  <[email protected]>
-	MACS 3.0.0a5
+2021-02-07  Tao Liu  <[email protected]>
+	MACS 3.0.0a6
 
 	* New features:
 
@@ -19,7 +19,7 @@
 	6) MACS tag-shifting model has been refined. Now it will use a
 	naive peak calling approach to find ALL possible paired peaks at +
 	and - strand, then use all of them to calculate the
-	cross-correlation.
+	cross-correlation. (a related bug has been fix #442)
 
 	7) Call variants in peak regions directly from BAM files. The 
 	function was originally developed under code name SAPPER. Now 

MACS3/Signal/Pileup.pyx

@@ -1,6 +1,6 @@
 # cython: language_level=3
 # cython: profile=True
-# Time-stamp: <2020-11-28 17:14:02 Tao Liu>
+# Time-stamp: <2021-02-05 16:31:53 Tao Liu>
 
 """Module Description: For pileup functions.
 
@@ -703,7 +703,7 @@ cpdef naive_call_peaks ( list pv_array, float min_v, float max_v = 1e30, int max
         except:
             break
         x += 1                  # index for the next point
-        if v >= min_v:
+        if v > min_v:
             peak_content = [ ( pre_p , p, v ), ]
             pre_p = p
             break               # found the first range above min_v
@@ -714,7 +714,7 @@ cpdef naive_call_peaks ( list pv_array, float min_v, float max_v = 1e30, int max
         # continue scan the rest regions
         p = psn()
         v = vsn()
-        if v < min_v: # not be detected as 'peak'
+        if v <= min_v: # not be detected as 'peak'
             pre_p = p
             continue
         # for points above min_v

MACS3/Utilities/Constants.py

@@ -1,4 +1,4 @@
-MACS_VERSION = "3.0.0a5"
+MACS_VERSION = "3.0.0a6"
 MAX_PAIRNUM = 1000
 MAX_LAMBDA  = 100000
 FESTEP      = 20

README.md

@@ -34,9 +34,9 @@ make sure that the main branch passes unit testing on certain
 functions and subcommands to reproduce the correct outputs. We will
 add more new features in the future.**
 
-## Recent Changes for MACS (3.0.0a5)
+## Recent Changes for MACS (3.0.0a6)
 
-### 3.0.0a5
+### 3.0.0a6
 	* New features
 
 	1) Speed/memory optimization.  Use the cykhash to replace python
@@ -56,7 +56,7 @@ add more new features in the future.**
     6) MACS tag-shifting model has been refined. Now it will use a
     naive peak calling approach to find ALL possible paired peaks at +
     and - strand, then use all of them to calculate the
-    cross-correlation.
+    cross-correlation. (a related bug has been fix #442)
 
     7) Call variants in peak regions directly from BAM files. The
 	function was originally developed under code name SAPPER. Now