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issue #1186 - don't return conversion_tool=None as will cause Liftove…
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…rRun failure later
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davmlaw committed Oct 23, 2024
1 parent b570657 commit 7f59722
Showing 1 changed file with 5 additions and 7 deletions.
12 changes: 5 additions & 7 deletions snpdb/liftover.py
Original file line number Diff line number Diff line change
Expand Up @@ -296,27 +296,25 @@ def _liftover_using_source_variant_coordinate(allele, source_genome_build: Genom
(settings.LIFTOVER_BCFTOOLS_ENABLED, AlleleConversionTool.BCFTOOLS_LIFTOVER, True),
]

conversion_tool = None
for enabled, potential_conversion_tool, require_reference_match in options:
for enabled, conversion_tool, require_reference_match in options:
if enabled:
if AlleleLiftover.has_existing_failure(allele, dest_genome_build, potential_conversion_tool):
if AlleleLiftover.has_existing_failure(allele, dest_genome_build, conversion_tool):
continue # Skip as already failed liftover method to desired build

if variant_errors_str:
yield potential_conversion_tool, None, variant_errors_str
yield conversion_tool, None, variant_errors_str
continue

if require_reference_match:
calculated_ref = variant_coordinate.calculated_reference(source_genome_build)
if calculated_ref != variant_coordinate.ref:
error_message = f"reference='{variant_coordinate.ref}' not equal to calculated ref from genome {calculated_ref}"
yield potential_conversion_tool, None, error_message
yield conversion_tool, None, error_message
continue

conversion_tool = potential_conversion_tool
yield conversion_tool, variant_coordinate, None
break # Just want 1st one

yield conversion_tool, variant_coordinate, None


def allele_can_attempt_liftover(allele, genome_build) -> bool:
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