added method to set cut_intervals

hicexplorer/HiCMatrix.py

@@ -196,6 +196,20 @@ def fillLowerTriangle(matrix):
 
         return matrix
 
+    def setCutIntervals(self, cut_intervals):
+        """
+        Replace the cut_intervals of a matrix
+        """
+
+        # check that the matrix is squared
+        if len(cut_intervals) != self.matrix.shape[0]:
+            raise Exception("Length of cut_intervals {} does not match the "
+                            "matrix size {}".format(len(cut_intervals), self.matrix.shape))
+
+        self.cut_intervals = cut_intervals
+        self.interval_trees, self.chrBinBoundaries = \
+            self.intervalListToIntervalTree(self.cut_intervals)
+
     def setMatrix(self, matrix, cut_intervals):
         """
         Initialize a matrix with a given matrix
@@ -206,6 +220,9 @@ def setMatrix(self, matrix, cut_intervals):
         # check that the matrix is squared
         if matrix.shape[0] != matrix.shape[1]:
             raise Exception("Matrix is not squared. Shape is {}".format(matrix.shape))
+        if len(cut_intervals) != matrix.shape[0]:
+            raise Exception("Length of cut_intervals {} does not match the matrix size {}".format(len(cut_intervals),
+                                                                                                      matrix.shape))
         self.matrix = matrix
         self.cut_intervals = cut_intervals
         self.interval_trees, self.chrBinBoundaries = \