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open2c · Mar 29, 2022 · 8ff00b8 · 8ff00b8
1 parent c518556
commit 8ff00b8
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Showing 2 changed files with 10 additions and 6 deletions.
diff --git a/pairtools/_dedup.pyx b/pairtools/_dedup.pyx
@@ -163,14 +163,16 @@ cdef class OnlineDuplicateDetector(object):
             self.keep_parent_id = 0
         else:
             self.keep_parent_id = 1
+            self.parent_idxs = np.zeros(0, np.int32)
+
         self.N = 0
         self.c1 = np.zeros(0, np.int32)
         self.c2 = np.zeros(0, np.int32)
         self.p1 = np.zeros(0, np.int32)
         self.p2 = np.zeros(0, np.int32)
         self.s1 = np.zeros(0, np.int32)
         self.s2 = np.zeros(0, np.int32)
-        self.parent_idxs = np.zeros(0, np.int32)
+
         self.rm = np.zeros(0, np.int8)
         if method == "max":
             self.methodid = 0
@@ -198,13 +200,13 @@ cdef class OnlineDuplicateDetector(object):
         self.s2 = self.s2[self.low:]
         pastrm = self.rm[:self.low]
         self.rm = self.rm[self.low:]
-        pastidx = self.parent_idxs[:self.low]
         self.high = self.high-self.low
         self.N = self.N - self.low
         self.low = 0
         if self.returnData == 1:
             return ret
         if self.keep_parent_id == 1: # Return parent readIDs alongside with duplicates mask:
+            pastidx = self.parent_idxs[:self.low]
             return pastrm, pastidx
         return pastrm
 
@@ -265,7 +267,8 @@ cdef class OnlineDuplicateDetector(object):
                     (self.s2[self.low] == self.s2[self.high]) and
                     extraCondition):
                 self.rm[self.high] = 1
-                self.parent_idxs[self.high] = self.low
+                if self.keep_parent_id == 1:
+                    self.parent_idxs[self.high] = self.low
                 self.high += 1
                 continue
             self.high += 1
@@ -280,7 +283,8 @@ cdef class OnlineDuplicateDetector(object):
         self.s1 = np.concatenate([self.s1, s1])
         self.s2 = np.concatenate([self.s2, s2])
         self.rm = np.concatenate([self.rm, np.zeros(len(c1), dtype=np.int8)])
-        self.parent_idxs = np.concatenate([self.parent_idxs, np.zeros(len(c1), dtype=np.int32)])
+        if self.keep_parent_id == 1:
+            self.parent_idxs = np.concatenate([self.parent_idxs, np.zeros(len(c1), dtype=np.int32)])
         self.N = self.N + len(c1)
         return self._run(finish=False)
 

diff --git a/requirements.txt b/requirements.txt
@@ -2,6 +2,6 @@ cython
 numpy>=1.10
 nose>=1.3
 click>=6.6
-scipy
-pandas
+scipy>=1.8.0
+pandas>=1.3.4
 pysam>=0.15.0