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Commits on Mar 9, 2026
Merge pull request #179 from liberu-genealogy/copilot/fix-reference-sequences-test
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Fix testGetAllReferenceSequences by providing 3 mock HTTP responses for 3 assemblies
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Merge pull request #178 from liberu-genealogy/copilot/fix-phar-archive-errors-another-one
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Fix CI failures: PharData registry conflicts, GSA resource contamination, discrepant SNPs test format
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Merge pull request #177 from liberu-genealogy/copilot/fix-phar-archive-errors-again
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Fix test failures: low_quality_snps.tsv.gz, PharData, rsid in XY dedup, merge thresholds
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Initial plan: fix all test failures
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Merge pull request #176 from liberu-genealogy/copilot/fix-test-failures
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fix: address 16 failing tests - build property, setSnps, merge, reader, QC
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Merge pull request #175 from liberu-genealogy/copilot/fix-test-failures-in-resources
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Fix 4 failing tests: GSA resources, reference sequence loading, and sex determination
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Merge pull request #174 from liberu-genealogy/copilot/fix-unclosed-brace-error
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Fix ParseError: add missing closing brace for SNPs class in SNPs.php
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Merge pull request #173 from liberu-genealogy/copilot/fix-phar-archive-errors
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Fix multiple test failures: PharData, DataFrame, sort order, dedup, merge, reader
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Merge pull request #172 from liberu-genealogy/copilot/fix-rest-api-404-error
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Fix REST API 404: Use correct Ensembl server URL and fix assembly name normalization in remap()
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Merge pull request #171 from liberu-genealogy/copilot/fix-phpunit-runtime-errors
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Fix ReferenceSequence duplicate getId/getID method and finalize all fixes
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Address code review: cleanup temp file, fix getBuild() length check, add getChipClusters() alias, fix merge() return type, improve merge() to return results array
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Fix multiple PHPUnit test failures: TypeError, missing methods, CSV indexing, and more
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Update PHP versions in GitHub Actions workflow
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Merge pull request #170 from liberu-genealogy/copilot/add-tests-workflow-and-badge
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Fix tests, add CI workflow and README badge
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Initial plan for tests workflow, badge, and fixes
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