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veff.py: in-frame complex variants (MNP+INDEL) return literal "TODO" string as effect — invalid scientific output Label issues #212: Issue #1315 opened by Tanisha127
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cnv_frq.py Hardcodes X-Chromosome Sex-Linked Ploidy Assumption — Breaks CNV Frequency Analysis for Non-Gambiae Species Label issues #211: Issue #1313 opened by khushthecoder
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ipinfo Location Check Silently Swallows All Network Errors With No Logging or Fallback Notification Label issues #210: Issue #1311 opened by kunal-10-cloud
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dask.config.set() at Module Import Time in ag3.py Silently Modifies Global Dask Configuration Label issues #209: Issue #1308 opened by khushthecoder
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sys.setrecursionlimit(10_000) in hapclust/dipclust Permanently Alters Global Python State Label issues #208: Issue #1305 opened by kunal-10-cloud
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Cloud Storage Access (GCS/S3) Has No Retry, Backoff, or Timeout Configuration Label issues #207: Issue #1303 opened by khushthecoder
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CI Coverage Workflow Has Two Blind Spots — Excludes Root Modules and Uses Outdated Codecov Action Label issues #206: Issue #1301 opened by kunal-10-cloud
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Integration Test and Notebook CI Workflows Use Hardcoded GCS Cache Key From September 2024 Label issues #205: Issue #1296 opened by kunal-10-cloud
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Unsanitized User Input Passed to DataFrame.eval() Enables Arbitrary Code Execution Label issues #204: Issue #1292 opened by kunal-10-cloud
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No Public API to Clear or Inspect In-Memory Caches — Users Cannot Reclaim Memory in Long-Running Sessions Label issues #203: Issue #1289 opened by khushthecoder
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diversity_stats doesn't have a max_cohort_size parameter Label issues #202: Issue #1288 opened by jonbrenas
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fix: geneset() and snp_dataset() are deprecated but emit no DeprecationWarning Label issues #201: Issue #1285 opened by Tanisha127
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snp_calls_to_vcf() silently drops requested FORMAT fields when underlying data arrays don't exist Label issues #200: Issue #1283 opened by Yashsingh045
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snp_calls_to_vcf() — Python-level per-sample loop creates severe performance bottleneck for large cohorts Label issues #199: Issue #1280 opened by khushthecoder
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S3 references in the docstring for Pf8 Label issues #198: Issue #1279 opened by jonbrenas
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_cache_locate_site_class can grow without bound despite _LOCATE_SITE_CLASS_CACHE_MAXSIZE constant Label issues #197: Issue #1276 opened by khushthecoder
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geneset() and snp_dataset() are deprecated but don't warn users Label issues #196: Issue #1273 opened by ZiadXI
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plot_samples_interactive_map returns an error when the data contains colony data and no other unassigned samples Label issues #195: Issue #1268 opened by jonbrenas
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Improve API and methods discoverability for agents and natural‑language interfaces Label issues #194: Issue #1262 opened by caiocrocha
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Replace assert Statements with Proper Runtime Validation in Production Code Label issues #193: Issue #1259 opened by khushthecoder
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Broken image URLs in docs Label issues #192: Issue #1247 opened by ahernank
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Improve LRU cache test coverage by validating eviction order in load_genome_seq (test_veff.py) Label issues #191: Issue #1244 opened by simplyshree
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Created tests/conftest.py with mocks for all missing dependencies to allow pytest to run tests. Label issues #190: Issue #1242 opened by karthik642006
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Add End-to-End Usage Examples and Real-World Analysis Workflow in README Label issues #189: Issue #1238 opened by lovelymahor
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Standardize test randomization using np.random Label issues #188: Issue #1237 opened by Yashsingh045
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