Pass exon annotations first when projecting transcript queries

ruranges/numpy.py

@@ -147,8 +147,9 @@ def map_to_global(
     """
     Vectorised transcript-to-genome projection.
 
-    All arrays must be 1-D and already sorted per transcript by
-    (local_start).  The *strand* arrays encode '+' as True and '−' as False.
+    All arrays must be 1-D. Each table must be sorted by transcript ID and
+    local start. The first table contains queries; the ``*2`` arrays contain
+    the exon annotation. The *strand* arrays encode '+' as True and '−' as False.
 
     Returns
     -------
@@ -162,8 +163,8 @@ def map_to_global(
 
     return _dispatch_map_global_binary(
         "map_to_global_numpy",
-        groups,  starts,  ends,  strand,
         groups2, starts2, ends2, strand2,
+        groups,  starts,  ends,  strand,
         chr_code2, genome_start2, genome_end2,
         sort_output=sort_output,
     )
@@ -1637,7 +1638,7 @@ def _dispatch_map_global_binary(
     ex_genome_end_u = _to_signed(ex_genome_end_arr, name="genome_end2", target=pos_t)
 
     grp_orig = np.asarray(ex_tx).dtype if ex_tx is not None else np.dtype(np.uint32)
-    pos_orig = ex_start.dtype
+    pos_orig = q_start_arr.dtype
     rust_fn, _, _ = _resolve_rust_fn(prefix, _CORE_GROUP_DTYPE, pos_t)
     raw = rust_fn(
         ex_tx_u,

tests/test_map_to_global.py

@@ -0,0 +1,67 @@
+"""Query rows map through the exon table supplied by the ``*2`` arguments."""
+import numpy as np
+import pytest
+
+from ruranges.numpy import map_to_global
+
+
+@pytest.mark.parametrize("forward", [True, False])
+@pytest.mark.parametrize("query_forward", [True, False])
+@pytest.mark.parametrize("dtype", [np.int32, np.int64, np.uint64])
+def test_query_spanning_two_exons(dtype, forward, query_forward):
+    genome_starts = [100, 200] if forward else [200, 100]
+    idx, starts, ends, strand = map_to_global(
+        starts=np.array([5], dtype=dtype),
+        ends=np.array([15], dtype=dtype),
+        groups=np.array([7]),
+        strand=np.array([query_forward]),
+        starts2=np.array([0, 10]),
+        ends2=np.array([10, 20]),
+        groups2=np.array([7, 7]),
+        chr_code2=np.array([1, 1]),
+        genome_start2=np.array(genome_starts),
+        genome_end2=np.array(genome_starts) + 10,
+        strand2=np.array([forward, forward]),
+    )
+    np.testing.assert_array_equal(idx, [0, 0])
+    np.testing.assert_array_equal(starts, [105, 200] if forward else [200, 105])
+    np.testing.assert_array_equal(ends, [110, 205] if forward else [205, 110])
+    np.testing.assert_array_equal(strand, [forward == query_forward] * 2)
+    assert starts.dtype == ends.dtype == np.dtype(dtype)
+
+
+def test_equal_query_and_exon_counts_do_not_exchange_local_coordinates():
+    idx, starts, ends, strand = map_to_global(
+        starts=np.array([5, 15]), ends=np.array([10, 20]),
+        groups=np.array([0, 0]), strand=np.array([True, False]),
+        starts2=np.array([0, 10]), ends2=np.array([10, 20]),
+        groups2=np.array([0, 0]), strand2=np.array([True, True]),
+        chr_code2=np.array([1, 1]),
+        genome_start2=np.array([100, 200]), genome_end2=np.array([110, 210]),
+    )
+    np.testing.assert_array_equal(idx, [0, 1])
+    np.testing.assert_array_equal(starts, [105, 205])
+    np.testing.assert_array_equal(ends, [110, 210])
+    np.testing.assert_array_equal(strand, [True, False])
+
+
+@pytest.mark.parametrize("shift", [0, 2**32])
+def test_query_attribution_across_transcripts_with_strided_inputs(shift):
+    def view(values, dtype=np.int64):
+        storage = np.zeros(2 * len(values), dtype=dtype)
+        storage[::2] = values
+        return storage[::2]
+
+    idx, starts, ends, strand = map_to_global(
+        starts=view([2, 4, 3]), ends=view([5, 7, 6]),
+        groups=view([1, 1, 2]), strand=view([True, False, True], bool),
+        starts2=view([0, 0]), ends2=view([10, 10]),
+        groups2=view([1, 2]), strand2=view([True, False], bool),
+        chr_code2=view([1, 2]),
+        genome_start2=view([shift + 100, shift + 200]),
+        genome_end2=view([shift + 110, shift + 210]),
+    )
+    np.testing.assert_array_equal(idx, [0, 1, 2])
+    np.testing.assert_array_equal(starts, np.array([102, 104, 204]) + shift)
+    np.testing.assert_array_equal(ends, np.array([105, 107, 207]) + shift)
+    np.testing.assert_array_equal(strand, [True, False, False])