Table.coordinate_system and Table.interval_type are silently ignored by spatial-predicate transpilation — Closes #88

[conradbzura]

Summary

Make INTERSECTS, CONTAINS, and WITHIN honor Table.coordinate_system and Table.interval_type so tables that store intervals in non-default conventions (e.g. VCF-style 1-based closed) produce correct SQL. Previously the table side of every spatial comparison was hard-coded for 0-based half-open columns, so any non-default Table configuration silently produced off-by-one results in both range-literal and column-join forms; SpatialSetPredicate (INTERSECTS ANY/ALL) inherited the same bug because it routes through the same helper.

The fix introduces three private helpers in BaseGIQLGenerator that wrap raw start/end column expressions to yield their canonical 0-based half-open equivalents, then wires those helpers into _generate_range_predicate and _generate_column_join. The literal side already arrives in canonical form via RangeParser.to_zero_based_half_open, so once both sides are canonicalized the existing comparison operators (<, >, <=, >=) are correct without per-operator branching.

Conversion table the helpers implement:

coordinate_system	interval_type	start_canonical	end_canonical
0based	half_open	start_col	end_col
0based	closed	start_col	(end_col + 1)
1based	half_open	(start_col - 1)	(end_col - 1)
1based	closed	(start_col - 1)	end_col

DISTANCE and NEAREST still ignore coordinate_system and conflate interval_type with bedtools-compatibility math; that is tracked separately in #89 and out of scope here.

Closes #88

Proposed changes

src/giql/generators/base.py

Add three helpers near _get_column_refs:

• _resolve_table(column_ref, table_name=None) — resolve the Table config that backs a column reference, mirroring the alias-resolution logic of _get_column_refs so each side of a column-join can be canonicalized independently.
• _canonical_start(raw_start, table) — staticmethod; wrap a raw start column expression to yield canonical 0-based half-open start. Returns (start_col - 1) for 1-based tables, the raw expression otherwise.
• _canonical_end(raw_end, table) — staticmethod; wrap a raw end column expression to yield canonical 0-based half-open end. Returns (end_col + 1) for 0-based-closed, (end_col - 1) for 1-based-half-open, raw expression for 0-based-half-open and 1-based-closed.

Modify two existing methods:

• _generate_range_predicate — call _resolve_table(column_ref, self._current_table), pass the result through _canonical_start / _canonical_end, then run the unchanged comparison-operator branches.
• _generate_column_join — same pattern, but resolve a Table for each side independently to support cross-convention joins.

tests/generators/test_base.py

Add four fixtures and eleven tests asserting the canonicalization behavior for every (coordinate_system, interval_type) combination across all three predicates and both forms (range-literal and column-join), plus the SpatialSetPredicate flow-through. Tests follow the BDD naming pattern test_<method>_should_<outcome>_when_<condition> and the AAA structure with Given/When/Then docstrings.

Test cases

#	Test Suite	Given	When	Then	Coverage Target
1	TestBaseGIQLGenerator	A 1-based-closed table	INTERSECTS is called with a literal range	The table-side start is wrapped as (start - 1) and end stays raw	INTERSECTS literal under 1-based-closed
2	TestBaseGIQLGenerator	A 1-based-closed table	CONTAINS is called with a literal range	The table-side start is wrapped as (start - 1) and end stays raw	CONTAINS literal under 1-based-closed
3	TestBaseGIQLGenerator	A 1-based-closed table	WITHIN is called with a literal range	The table-side start is wrapped as (start - 1) and end stays raw	WITHIN literal under 1-based-closed
4	TestBaseGIQLGenerator	A 0-based-half-open table joined against a 1-based-closed table	INTERSECTS is called between columns from each table	Each side is canonicalized independently — 1-based-closed side gets (start - 1), default side stays raw	INTERSECTS column-join under mixed conventions
5	TestBaseGIQLGenerator	A table declared with explicit defaults coordinate_system="0based" and interval_type="half_open"	INTERSECTS is called with a literal range	Raw start/end columns are emitted with no arithmetic wrappers	Regression guard for default Table
6	TestBaseGIQLGenerator	A 0-based-closed table	INTERSECTS is called with a literal range	The table-side end is wrapped as (end + 1) and start stays raw	INTERSECTS literal under 0-based-closed
7	TestBaseGIQLGenerator	A 1-based-half-open table	INTERSECTS is called with a literal range	Both table-side endpoints are wrapped by subtracting 1	INTERSECTS literal under 1-based-half-open
8	TestBaseGIQLGenerator	A 0-based-half-open table joined against a 1-based-closed table	CONTAINS is called between columns from each table	Each side is canonicalized independently while comparison operators stay <= / >=	CONTAINS column-join under mixed conventions
9	TestBaseGIQLGenerator	A 0-based-half-open table joined against a 1-based-closed table	WITHIN is called between columns from each table	Each side is canonicalized independently while comparison operators stay >= / <=	WITHIN column-join under mixed conventions
10	TestBaseGIQLGenerator	A 1-based-closed table	CONTAINS is called with a point query chr1:1500	The point-query branch fires and the table-side start is wrapped as (start - 1)	CONTAINS point-query under 1-based-closed
11	TestBaseGIQLGenerator	A 1-based-closed table	INTERSECTS ANY is called with multiple literal ranges	Each OR-disjunct is canonicalized independently with (start - 1) on the table side	SpatialSetPredicate flow-through under 1-based-closed