Merge pull request open2c#6 from mirnylab/master

merge latest from mirnylab-master

cooltools/dotfinder.py

@@ -1770,7 +1770,9 @@ def clustering_step(
     df = pd.merge(
         scores_df, pixel_clust_df, how="left", left_index=True, right_index=True
     )
-
+    #prevents scores_df categorical values (all chroms, including chrM)
+    df['chrom1'] = df['chrom1'].astype(str)
+    df['chrom2'] = df['chrom2'].astype(str)
     # report only centroids with highest Observed:
     chrom_clust_group = df.groupby(["chrom1", "chrom2", "c_label"])
     centroids = df.loc[chrom_clust_group[obs_raw_name].idxmax()]

cooltools/lib/common.py

@@ -30,16 +30,16 @@ def assign_supports(features, supports, labels=False, suffix=""):
     for i, region in enumerate(supports):
         # single-region support
         if len(region) == 3:
-            sel = (features[c] == region[0]) & (features[e] >= region[1])
+            sel = (features[c] == region[0]) & (features[e] > region[1])
             if region[2] is not None:
                 sel &= features[s] < region[2]
         # paired-region support
         elif len(region) == 2:
             region1, region2 = region
-            sel1 = (features[c] == region1[0]) & (features[e] >= region1[1])
+            sel1 = (features[c] == region1[0]) & (features[e] > region1[1])
             if region1[2] is not None:
                 sel1 &= features[s] < region1[2]
-            sel2 = (features[c] == region2[0]) & (features[e] >= region2[1])
+            sel2 = (features[c] == region2[0]) & (features[e] > region2[1])
             if region2[2] is not None:
                 sel2 &= features[s] < region2[2]
             sel = sel1 | sel2

cooltools/snipping.py

@@ -436,6 +436,13 @@ def __init__(self, clr, expected):
         else:
             raise ValueError("Expected dataframe has no columns.")
 
+        try:
+            for region, group in self.expected.groupby(self.regions_columns):
+                assert group.shape[0]==np.diff(self.clr.extent(region))[0]
+        except AssertionError:
+            raise ValueError("Region shape mismatch between expected and cooler. "
+                             "Are they using the same resolution?")
+
         self.binsize = self.clr.binsize
         self.offsets = {}