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Improve error messaging when haplotypes_frequencies_advanced yields no cohorts Label issues #163: Issue #1170 opened by karthik642006
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Add list_extra_metadata() and improve clear_extra_metadata() to prevent silent metadata accumulation Label issues #162: Issue #1168 opened by khushthecoder
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Temporarily commenting phenotype tests in tests/integration/test_ag3.py Label issues #161: Issue #1167 opened by jonbrenas
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ML-Based Taxon Classification for MalariaGEN Data Label issues #160: Issue #1165 opened by Aadik1ng
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Feature Request: Always return Plotly figure objects from plot_* methods to enable programmatic customization and saving Label issues #159: Issue #1162 opened by khushthecoder
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Bug: phenotypes.py swallows all exceptions via broad except Exception, silently masking data and logic errors Label issues #158: Issue #1160 opened by khushthecoder
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Error accessing roh_hmm Label issues #157: Issue #1151 opened by KellyLBennett
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Add type hints and comprehensive docstrings to utility functions in util.py Label issues #156: Issue #1141 opened by aadi-9
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Things that should improve Label issues #155: Issue #1139 opened by godswillokafor243-lab
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veff.py has no unit tests Label issues #154: Issue #1138 opened by RajdeepKushwaha5
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veff.py: in-frame complex variants return literal "TODO" string as effect label Label issues #153: Issue #1132 opened by sallykinyua
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sample_indices parameter missing from multiple methods that internally call sample_metadata Label issues #152: Issue #1126 opened by noir4201
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# Feature Request: Introduce a Structured Query Abstraction Layer to Support API Extensions and Natural Language Interfaces Label issues #151: Issue #1123 opened by rajat552
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CONTRIBUTING.md: incorrect pipx documentation link Label issues #150: Issue #1120 opened by star-lord1234
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plot_haplotypes_frequencies.ipynb: ag3 used instead of af1 in Af1 section Label issues #149: Issue #1117 opened by star-lord1234
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Add dataset summary helper and exploratory notebook for mosquito taxonomy analysis Label issues #148: Issue #1115 opened by PrakharLal
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Hash PLINK export filenames by content-affecting selection parameters to prevent collisions Label issues #147: Issue #1113 opened by rehanxt5
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Plasmodium _subset_genome_sequence_region has the same truthiness bug Label issues #146: Issue #1108 opened by Gopisokk
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Fix contributor guide link and CI version details Label issues #145: Issue #1105 opened by NayerBasim
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Preserve sample_query_options during cohort query normalisation Label issues #144: Issue #1100 opened by kshirajahere
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Setup instructions in CONTRIBUTING.md fail with ModuleNotFoundError: pytest_cases on fresh clone Label issues #143: Issue #1097 opened by Stu-ops
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Add example notebook for exploring mosquito species distribution Label issues #142: Issue #1094 opened by priyarai121
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Add example notebook for visualizing mosquito sample geographic distribution Label issues #141: Issue #1093 opened by priyarai121
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year=-1 sentinel value in lab cross samples causes crashes and silent NaN values in sample_metadata() downstream analysis Label issues #140: Issue #1092 opened by sallykinyua
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Docs: LINUX_SETUP.md relies on Ubuntu-specific PPA Label issues #139: Issue #1091 opened by Schronding
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