Update PairedEndTrack.pyx

Fix a bug while dealing with some chromosome only contains one read (pair). The size of new_locs after filtering dups should +1.
lw3259111 · Oct 9, 2015 · 6d2bedb · 6d2bedb
1 parent a3438e8
commit 6d2bedb
Showing 1 changed file with 5 additions and 5 deletions.
diff --git a/MACS2/IO/PairedEndTrack.pyx b/MACS2/IO/PairedEndTrack.pyx
@@ -298,11 +298,11 @@ cdef class PETrackI:
             i_dup = 0
             locs = self.__locations[k]
             size = locs.shape[0]
-            if size < 1:
+            if size <= 1:
                 new_locs = locs
             else:
-                new_locs = np.zeros(self.__pointer[k], dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
-                dup_locs = np.zeros(self.__pointer[k], dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
+                new_locs = np.zeros(self.__pointer[k] + 1, dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
+                dup_locs = np.zeros(self.__pointer[k] + 1, dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
                 i_new += 1
                 n = 1
 
@@ -385,10 +385,10 @@ cdef class PETrackI:
             i_new = 0
             locs = self.__locations[k]
             size = locs.shape[0]
-            if size < 1:
+            if size <= 1:
                 new_locs = locs
             else:
-                new_locs = np.zeros( self.__pointer[k], dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
+                new_locs = np.zeros( self.__pointer[k] + 1, dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
                 i_new += 1
                 n = 1                # the number of tags in the current location