Merge pull request #41 from deeptools/revert-40-fixfit_cut_intervals

Revert "Fix fit cut intervals"
deeptools · Jul 19, 2021 · c44f5ed · c44f5ed
2 parents 6ca77d1 + 4a9d523
commit c44f5ed
Showing 1 changed file with 2 additions and 3 deletions.
diff --git a/hicmatrix/HiCMatrix.py b/hicmatrix/HiCMatrix.py
@@ -13,7 +13,6 @@
 from intervaltree import IntervalTree, Interval
 import cooler
 import time
-from collections import Counter
 
 from .utilities import toBytes
 from .utilities import toString
@@ -170,7 +169,7 @@ def getBinSize(self):
                 return self.bin_size
             # If there are more bins, the diff will be compared
             # to the median of the differences between starts
-            median = int(np.median(np.concatenate([np.diff([start for chro, start, end, extra in self.cut_intervals if chro == cur_chrom]) for cur_chrom, nb in Counter(chrom).items() if nb > 1])))
+            median = int(np.median(np.diff(start)))
 
             # check if the bin size is
             # homogeneous
@@ -335,7 +334,7 @@ def fit_cut_intervals(cut_intervals):
             return cut_intervals
         chrom, start, end, extra = zip(*cut_intervals)
 
-        median = int(np.median(np.concatenate([np.diff([start for chro, start, end, extra in cut_intervals if chro == cur_chrom]) for cur_chrom, nb in Counter(chrom).items() if nb > 1])))
+        median = int(np.median(np.diff(start)))
         diff = np.array(end) - np.array(start)
         # check if the bin size is homogeneous
         if len(np.flatnonzero(diff != median)) > (len(diff) * 0.01):