fix: hotfix for indexer usage

d-laub · d-laub · commit 5b1eb9701ed1 · 2025-04-01T10:38:32.000-07:00
diff --git a/python/genvarloader/_dataset/_impl.py b/python/genvarloader/_dataset/_impl.py
@@ -898,9 +898,8 @@ def haplotype_lengths(
             samples = slice(None)
         idx = (regions, samples)
 
-        idx, squeeze, out_reshape = self._parse_getitem_idx(idx)
+        ds_idx, squeeze, out_reshape = self._idxer.parse_idx(idx)
 
-        ds_idx = self._idxer[idx]
         r_idx, _ = np.unravel_index(ds_idx, self.full_shape)
 
         # (b)
diff --git a/python/genvarloader/_dataset/_indexing.py b/python/genvarloader/_dataset/_indexing.py
@@ -168,7 +168,7 @@ def parse_idx(
             or (isinstance(samples, np.ndarray) and is_dtype(samples, np.str_))
             or (
                 isinstance(samples, Sequence)
-                and isinstance(next(chain.from_iterable(samples)), str)
+                and isinstance(next(chain.from_iterable(samples)), str)  # type: ignore
             )
         ):
             s_idx = self.s2i_map.get(samples)
diff --git a/python/genvarloader/_dataset/_reconstruct.py b/python/genvarloader/_dataset/_reconstruct.py
@@ -709,7 +709,7 @@ def write_transformed_track(
                     np.arange(n_samples, dtype=np.intp), "s -> (r s)", r=n_regions
                 )
                 ds_idx = np.ravel_multi_index((ir_idx, is_idx), idxer.full_shape)
-                ds_idx = idxer[ds_idx]
+                ds_idx = idxer.i2d_map[ds_idx]
                 r_idx, s_idx = np.unravel_index(ds_idx, idxer.full_shape)
 
                 pbar.set_description("Writing (decompressing)")

Original file line number	Diff line number	Diff line change
`@@ -168,7 +168,7 @@ def parse_idx(`
`168`	`168`	`or (isinstance(samples, np.ndarray) and is_dtype(samples, np.str_))`
`169`	`169`	`or (`
`170`	`170`	`isinstance(samples, Sequence)`
`171`		`- and isinstance(next(chain.from_iterable(samples)), str)`
	`171`	`+ and isinstance(next(chain.from_iterable(samples)), str) # type: ignore`
`172`	`172`	`)`
`173`	`173`	`):`
`174`	`174`	`s_idx = self.s2i_map.get(samples)`
Original file line number	Diff line number	Diff line change
`@@ -709,7 +709,7 @@ def write_transformed_track(`
`709`	`709`	`np.arange(n_samples, dtype=np.intp), "s -> (r s)", r=n_regions`
`710`	`710`	`)`
`711`	`711`	`ds_idx = np.ravel_multi_index((ir_idx, is_idx), idxer.full_shape)`
`712`		`- ds_idx = idxer[ds_idx]`
	`712`	`+ ds_idx = idxer.i2d_map[ds_idx]`
`713`	`713`	`r_idx, s_idx = np.unravel_index(ds_idx, idxer.full_shape)`
`714`	`714`
`715`	`715`	`pbar.set_description("Writing (decompressing)")`