Fix remove_variant to use position1 instead of position#260
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variant.position is not defined on base variants; variant.position1 is the correct attribute. This caused remove_variant to silently no-op on every call, leaving stale variants in ContigVariants. Adds regression tests in tests/test_variants/test_remove_variant.py. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Insertion.contains() expects an int (a reference position), but check_if_ins was passing the full variant object. This caused the method to always return None, silently failing to detect variants overlapping an insertion span. Adds regression tests in tests/test_variants/test_check_if_ins.py. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Fix/contig variants check if ins
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Merged with the other bug pr because they were related. |
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variant.position is not defined on base variants; variant.position1 is the correct attribute. This caused remove_variant to silently no-op on every call, leaving stale variants in ContigVariants.
Adds regression tests in tests/test_variants/test_remove_variant.py.