Merge pull request #557 from dmalzl/master

respect dtypes of input file

Author: Phlya

cooltools/api/rearrange.py

@@ -202,6 +202,8 @@ def rearrange_cooler(
         bins_old, view_df, new_chrom_col=new_chrom_col, orientation_col=orientation_col
     )
     logging.info("Creating a new cooler")
+    # fetching pixel dtypes to avoid implicit casts of count column
+    dtypes = clr.pixels().dtypes.to_dict()
     cooler.create_cooler(
         out_cooler,
         bins_new,
@@ -210,6 +212,7 @@ def rearrange_cooler(
             bin_mapping,
             chunksize=chunksize,
         ),
+        dtypes = dtypes,
         assembly=assembly,
         mode=mode,
         mergebuf=int(2e7),

tests/data/float_counts.cool

@@ -62,7 +62,7 @@ def test_rearrange_cooler(request):
 
     # III.
     # Check that when taking two chromosomes in a different order and inverting one,
-    # all is ax espected
+    # all is as espected
 
     reorder_invert_view = (
         orig_view.iloc[1::-1].assign(strand=["+", "-"]).reset_index(drop=True)
@@ -136,3 +136,15 @@ def test_rearrange_cooler(request):
         ::-1, :
     ]
     assert np.array_equal(old_trans_m, reordered_inverted_trans_m, equal_nan=True)
+
+    # IV.
+    # Check that pixel datatypes are propagated to output cooler
+    float_clr = cooler.Cooler(op.join(request.fspath.dirname, "data/float_counts.cool"))
+    new_view = bioframe.make_viewframe(float_clr.chromsizes)
+    rearrange_cooler(float_clr, new_view, "test_propagated_datatypes.cool")
+
+    propagate_clr = cooler.Cooler("test_propagated_datatypes.cool")
+    assert_frame_equal(
+        float_clr.pixels()[:], 
+        propagate_clr.pixels()[:]
+    )