gwaslab 3.4.48__py3-none-any.whl → 3.5.0__py3-none-any.whl

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Files changed (25) hide show
  1. gwaslab/bd_common_data.py +3 -1
  2. gwaslab/data/reference.json +10 -2
  3. gwaslab/g_Sumstats.py +24 -2
  4. gwaslab/g_vchange_status.py +1 -1
  5. gwaslab/g_version.py +2 -2
  6. gwaslab/hm_harmonize_sumstats.py +23 -7
  7. gwaslab/io_preformat_input.py +73 -8
  8. gwaslab/io_to_formats.py +5 -5
  9. gwaslab/qc_fix_sumstats.py +106 -7
  10. gwaslab/util_in_fill_data.py +20 -2
  11. gwaslab/util_in_get_sig.py +18 -2
  12. gwaslab/viz_aux_annotate_plot.py +75 -242
  13. gwaslab/viz_aux_quickfix.py +9 -2
  14. gwaslab/viz_aux_save_figure.py +2 -1
  15. gwaslab/viz_plot_compare_effect.py +48 -20
  16. gwaslab/viz_plot_miamiplot2.py +5 -1
  17. gwaslab/viz_plot_mqqplot.py +70 -20
  18. gwaslab/viz_plot_phe_heatmap.py +260 -0
  19. gwaslab/viz_plot_stackedregional.py +11 -4
  20. {gwaslab-3.4.48.dist-info → gwaslab-3.5.0.dist-info}/METADATA +1 -1
  21. {gwaslab-3.4.48.dist-info → gwaslab-3.5.0.dist-info}/RECORD +25 -24
  22. {gwaslab-3.4.48.dist-info → gwaslab-3.5.0.dist-info}/WHEEL +1 -1
  23. {gwaslab-3.4.48.dist-info → gwaslab-3.5.0.dist-info}/LICENSE +0 -0
  24. {gwaslab-3.4.48.dist-info → gwaslab-3.5.0.dist-info}/LICENSE_before_v3.4.39 +0 -0
  25. {gwaslab-3.4.48.dist-info → gwaslab-3.5.0.dist-info}/top_level.txt +0 -0
{gwaslab-3.4.48.dist-info → gwaslab-3.5.0.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: gwaslab
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- Version: 3.4.48
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+ Version: 3.5.0
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  Summary: A collection of handy tools for GWAS SumStats
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  Author-email: Yunye <yunye@gwaslab.com>
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  Project-URL: Homepage, https://cloufield.github.io/gwaslab/
{gwaslab-3.4.48.dist-info → gwaslab-3.5.0.dist-info}/RECORD RENAMED
@@ -1,25 +1,25 @@
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  gwaslab/__init__.py,sha256=7TKJaODdpeuQKibL7gIEa4MtyQ0pmrU-vIHQ-Et27lQ,2433
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- gwaslab/bd_common_data.py,sha256=qr6OMbBaTH2Smfu8347SO9NmF410tn8dq8pRGF5-OpY,13751
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+ gwaslab/bd_common_data.py,sha256=2voBqMrIsII1TN5T6uvyDax90fWcJK1Stmo1ZHNGGsE,13898
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  gwaslab/bd_config.py,sha256=TP-r-DPhJD3XnRYZbw9bQHXaDIkiRgK8bG9HCt-UaLc,580
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  gwaslab/bd_download.py,sha256=cDDk2C5IvjeAzvPvVYGTkI4Ss33DUtEDjGo8eAbQRvY,15663
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  gwaslab/bd_get_hapmap3.py,sha256=asNjQYeGfQi8u3jnfenRvDdKMs5ptql5wpcUzqMlwUI,3937
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  gwaslab/cache_manager.py,sha256=HOTnSkCOyGEPLRl90WT8D_6pAdI8d8AzenMIDGuCeWc,28113
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  gwaslab/g_Log.py,sha256=C3Zv-_6c3C9ms8bgQ-ytplz22sjk7euqXYkWr9zNeAs,1573
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  gwaslab/g_Phenotypes.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- gwaslab/g_Sumstats.py,sha256=U5la-fJCSTN8FNxXjcULcPH8MV9D6YgMaVFNesMTa_o,35854
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+ gwaslab/g_Sumstats.py,sha256=6bzc7Sf23fIZRP85h-hQJC8DsBl3YLZNBUKJaOboHJQ,36639
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  gwaslab/g_SumstatsPair.py,sha256=20snPb4SlI6ftMGVjgxAuyxsxYRQF-GzzlBSnoB-3Lo,8851
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  gwaslab/g_SumstatsT.py,sha256=u_DighLMnMxwTLnqm-B58pA0G6WXRj6pudPyKMVKjSU,2133
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  gwaslab/g_Sumstats_summary.py,sha256=FECvvFXJVKaCX5dggBvvk9YvJ6AbdbcLfjltysX7wEE,6380
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  gwaslab/g_meta.py,sha256=htWlgURWclm9R6UqFcX1a93WN27xny7lGUeyJZOtszQ,2583
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- gwaslab/g_vchange_status.py,sha256=jLoVzMJFhB5k_cJKzHuBNc2HZGBWydAunCNa0n_d54g,1923
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- gwaslab/g_version.py,sha256=kB6LiBYcRZElabjDUUEBhF5c5SVUq8vHO0pctDfBqkw,1886
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+ gwaslab/g_vchange_status.py,sha256=w3zsYYOcCaI3PTeboonvkQjudzUAfVIgATzRdiPViZs,1939
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+ gwaslab/g_version.py,sha256=ll9kIVGycz_99ofwzsFd_semBDePvcEjIqqCgWdVa_8,1885
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  gwaslab/hm_casting.py,sha256=FqP4EQl83Q2OKLw004OgLIvUH795TVCGwziLk5jsHqY,11368
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- gwaslab/hm_harmonize_sumstats.py,sha256=1hjUdle2DSKHGBp2BktfFqf-QHU_q2xWl_mPhiYc_ZA,78616
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+ gwaslab/hm_harmonize_sumstats.py,sha256=_sZ8soikAxDokw-dcr_CLguBB8OmTmPPS04MfmsJc_Q,79509
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  gwaslab/hm_rsid_to_chrpos.py,sha256=ODWREO0jPN0RAfNzL5fRzSRANfhiksOvUVPuEsFZQqA,6552
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- gwaslab/io_preformat_input.py,sha256=AZ43WGqVTzbo3XtClWhjRjsj6pBR9stw6JBL_TZ461U,20673
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+ gwaslab/io_preformat_input.py,sha256=J8Ny4OPMaLVdo2nP8lTM-c5A8LSdqphSrp9G4i9JjDQ,24097
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  gwaslab/io_read_ldsc.py,sha256=wsYXpH50IchBKd2dhYloSqc4YgnDkiwMsAweaCoN5Eo,12471
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  gwaslab/io_read_tabular.py,sha256=EG-C6KhCutt4J4LlOMgXnqzJvU-EZXzVhMvaDFnHrMM,2380
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- gwaslab/io_to_formats.py,sha256=m57dGoqmHzAE1E27j9YxYKVCA12_lKd1qCnZtp0WZLw,29401
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+ gwaslab/io_to_formats.py,sha256=8FmbQjWUIsz_V1Lb80TuwRIXKBgs5t42j25Znougk1Y,29401
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  gwaslab/io_to_pickle.py,sha256=HhePU0VcaGni0HTNU0BqoRaOnrr0NOxotgY6ISdx3Ck,1833
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  gwaslab/ldsc_irwls.py,sha256=83JbAMAhD0KOfpv4IJa6LgUDfQjp4XSJveTjnhCBJYQ,6142
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  gwaslab/ldsc_jackknife.py,sha256=XrWHoKS_Xn9StG1I83S2vUMTertsb-GH-_gOFYUhLeU,17715
@@ -28,7 +28,7 @@ gwaslab/ldsc_parse.py,sha256=MBnfgcWlV4oHp9MoDRh1mpilaHhAR15Af77hMFn4-5k,10564
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  gwaslab/ldsc_regressions.py,sha256=yzbGjgNV7u-SWXNPsh9S8y9mK97Bim_Nmad9G9V18ZU,30078
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  gwaslab/ldsc_sumstats.py,sha256=O0olsDxKlh1MJ1gAuEN1t40rxhajOEwOQ20ak7xoDrI,26245
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  gwaslab/qc_check_datatype.py,sha256=kW68uk4dTLOU2b1dHoVat6n0loundDysAjIqxsXW28Q,3379
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- gwaslab/qc_fix_sumstats.py,sha256=aTX5jf7MVpp6XTiP-rbEyaLAQFsn1gyH9vEH4SLH-GY,93199
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+ gwaslab/qc_fix_sumstats.py,sha256=rb1Iv05o0tYGGTiXXXJphkx-xVQNKAtlwkDfY-D0yPs,97979
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  gwaslab/run_script.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  gwaslab/util_abf_finemapping.py,sha256=LRcopjtkT-iXtKPAJIzR4qjPdhD7nrS_BGit4EW89FM,3054
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  gwaslab/util_ex_calculate_ldmatrix.py,sha256=Z_spxbq6SHDS0v84I59YTTF40iyLQIOZbt0dmEcNJjw,15417
@@ -47,40 +47,41 @@ gwaslab/util_in_calculate_gc.py,sha256=MWOXVzJv7SZx4i2_ncRiqsiEOADc7EfghaUzgGy4j
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  gwaslab/util_in_calculate_power.py,sha256=JfHJFg3tNF0f4NHgWlzVW2mSxCiP07mAHIyEfVfxTak,10360
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  gwaslab/util_in_convert_h2.py,sha256=a8Cbudt3xn9WP2bPc-7ysuowB-LYub8j8GeDXl7Lk7Q,6483
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  gwaslab/util_in_correct_winnerscurse.py,sha256=Gp--yAQ8MMzdkWIvXP9C1BHVjZc-YzqHfYWhAj19w9w,2110
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- gwaslab/util_in_fill_data.py,sha256=gdTwYA6FvBMnrtxAeL0lEj_Z0aGIoRNPScWDlJvZWeQ,14021
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+ gwaslab/util_in_fill_data.py,sha256=iVq5WLWwFI03v9HyvBanu5si3j2p-oyPFTl8jsX69xM,14693
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  gwaslab/util_in_filter_value.py,sha256=dY4X66N9A4MHCRHjPqLYFufMM91ggLRwUBf_nJYh8Lg,23605
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  gwaslab/util_in_get_density.py,sha256=kpKXH69acMkeYVG5vs-VbJC3COhmuLBfYco-wuOxgjc,3934
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- gwaslab/util_in_get_sig.py,sha256=9kq1GXacknO2YnVmsTli1GlPA728ASweTZ3UKm3Wszo,38783
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+ gwaslab/util_in_get_sig.py,sha256=53NOh7KueLY3vJPTNhhb37KPAIgLEfcP3k2zIV61lc4,39845
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  gwaslab/util_in_meta.py,sha256=5K9lIZcIgUy0AERqHy1GvMN2X6dp45JUUgopuDLgt4o,11284
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  gwaslab/util_in_snphwe.py,sha256=-KpIDx6vn_nah6H55IkV2OyjXQVXV13XyBL069WE1wM,1751
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- gwaslab/viz_aux_annotate_plot.py,sha256=UTOx-OpFsM_UVphBHxqQZwCFI8bjwwB6CMsgFbAfheQ,32215
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+ gwaslab/viz_aux_annotate_plot.py,sha256=i-Fvg_4H6LZvENM6F_yH9-sVSxjD_9LwVhlvgHusW6w,25006
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  gwaslab/viz_aux_chromatin.py,sha256=7cGmej5EkKO7fxR1b5w8r1oRRl9ofVzFRG52SCYWtz0,4109
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- gwaslab/viz_aux_quickfix.py,sha256=5XM-J9D2yp5FVbK6YQKEhSCqAYBLNWSQms9WjpXxVn8,18313
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+ gwaslab/viz_aux_quickfix.py,sha256=HnhVvY0GP0EN0gLJ-B11OYiE5PWDcdKGUpQ3QZeu0lE,18592
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  gwaslab/viz_aux_reposition_text.py,sha256=iRIP-Rkltlei068HekJcVubiqPrunBqvAoSQ1eHk04M,4304
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- gwaslab/viz_aux_save_figure.py,sha256=nL-aoE8Kg06h7FgleGRBIZjhI-6w5gpn3E1HWMwBig8,2664
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+ gwaslab/viz_aux_save_figure.py,sha256=GdUXNBOelsWqtTXm8pEZzeGGwDxHYnBkyrGwLOK16ew,2723
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  gwaslab/viz_plot_compare_af.py,sha256=qtXW45-Sq_ugK8ZfqBYMpmf58SKi3lB3YyHnzn_akcE,5344
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- gwaslab/viz_plot_compare_effect.py,sha256=lV-4KSQatTSsYqzEGGTkBu17I2VlVyVh1uJr-kCq630,49585
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+ gwaslab/viz_plot_compare_effect.py,sha256=60KlfRGj1TSc0-NCaInZ7GMiAUveXe4qDCjIW-RHJNE,51304
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  gwaslab/viz_plot_forestplot.py,sha256=xgOnefh737CgdQxu5naVyRNBX1NQXPFKzf51fbh6afs,6771
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  gwaslab/viz_plot_miamiplot.py,sha256=rCFEp7VNuVqeBBG3WRkmFAtFklbF79BvIQQYiSY70VY,31238
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- gwaslab/viz_plot_miamiplot2.py,sha256=Jg5j9qsr8gGydU8AOKU8xRZTNH_3QM8Nxv61Vh12aG0,15732
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- gwaslab/viz_plot_mqqplot.py,sha256=q_c_ZDRdirEcdHHnb030h7dTUWAFy9OVuzwbdCzZ3gU,64580
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+ gwaslab/viz_plot_miamiplot2.py,sha256=xiFCgFX8hEySmCJORpEurMVER9eEXQyy_Ik7mLkbi9g,16015
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+ gwaslab/viz_plot_mqqplot.py,sha256=nIwS3fMAXv_LVn7l9koSFZiZbcKCyuVq6Qg5fMzrEps,67049
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+ gwaslab/viz_plot_phe_heatmap.py,sha256=vCCPAiTyBBVklZahXG_zmyxXPgm0d7ArVha7A6gJaok,9514
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  gwaslab/viz_plot_qqplot.py,sha256=psQgVpP29686CEZkzQz0iRbApzqy7aE3GGiBcazVvNw,7247
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  gwaslab/viz_plot_regional2.py,sha256=tBoGox-4ngL5o_twdIjk_VW6Iam3JDyrPKuttm6_4Sg,36862
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  gwaslab/viz_plot_regionalplot.py,sha256=8u-5-yfy-UaXhaxVVz3Y5k2kBAoqzczUw1hyyD450iI,37983
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  gwaslab/viz_plot_rg_heatmap.py,sha256=PidUsgOiEVt6MfBPCF3_yDhOEytZ-I1q-ZD6_0pFrV4,13713
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- gwaslab/viz_plot_stackedregional.py,sha256=AoGMer73P3y-21A2qityrDX-_sIJFRgKzkm8i9zVxKA,16420
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+ gwaslab/viz_plot_stackedregional.py,sha256=IRugpwLjqKdwuSVTQtCM36Rk4Gpv6MxdsGIWVj6vk8w,16651
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  gwaslab/viz_plot_trumpetplot.py,sha256=ZHdc6WcVx0-oKoj88yglRkmB4bS9pOiEMcuwKW35Yvo,42672
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  gwaslab/data/formatbook.json,sha256=N2nJs80HH98Rsu9FxaSvIQO9J5yIV97WEtAKjRqYwiY,38207
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- gwaslab/data/reference.json,sha256=k8AvvgDsuLxzv-NCJHWvTUZ5q_DLAFxs1Th3jtL313k,11441
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+ gwaslab/data/reference.json,sha256=IrjwFnXjrpVUp3zYfcYClpibJE9Y-94gtrC1Aw8sXxg,12332
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  gwaslab/data/chrx_par/chrx_par_hg19.bed.gz,sha256=LocZg_ozhZjQiIpgWCO4EYCW9xgkEKpRy1m-YdIpzQs,83
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  gwaslab/data/chrx_par/chrx_par_hg38.bed.gz,sha256=VFW11MnQVC-Iu-ZGvUDcEhVpb-HVRsVTg-W-GNJyxP4,82
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  gwaslab/data/hapmap3_SNPs/hapmap3_db150_hg19.snplist.gz,sha256=qD9RsC5S2h6l-OdpW09DWXHIi2kcPebctMnhxt8mzfU,10282886
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  gwaslab/data/hapmap3_SNPs/hapmap3_db151_hg38.snplist.gz,sha256=Y8ZT2FIAhbhlgCJdE9qQVAiwnV_fcsPt72usBa7RSBM,10225828
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  gwaslab/data/high_ld/high_ld_hla_hg19.bed.gz,sha256=R7IkssKu0L4WwkU9SrS84xCMdrkkKL0gnTNO_OKbG0Y,219
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  gwaslab/data/high_ld/high_ld_hla_hg38.bed.gz,sha256=76CIU0pibDJ72Y6UY-TbIKE9gEPwTELAaIbCXyjm80Q,470
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- gwaslab-3.4.48.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
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- gwaslab-3.4.48.dist-info/LICENSE_before_v3.4.39,sha256=GhLOU_1UDEKeOacYhsRN_m9u-eIuVTazSndZPeNcTZA,1066
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- gwaslab-3.4.48.dist-info/METADATA,sha256=4Cqofc_AlsSBNtwKwiLBFiDtQsh8UUvWiM_XhBYksxw,7752
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- gwaslab-3.4.48.dist-info/WHEEL,sha256=Mdi9PDNwEZptOjTlUcAth7XJDFtKrHYaQMPulZeBCiQ,91
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- gwaslab-3.4.48.dist-info/top_level.txt,sha256=PyY6hWtrALpv2MAN3kjkIAzJNmmBTH5a2risz9KwH08,8
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- gwaslab-3.4.48.dist-info/RECORD,,
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+ gwaslab-3.5.0.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
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+ gwaslab-3.5.0.dist-info/LICENSE_before_v3.4.39,sha256=GhLOU_1UDEKeOacYhsRN_m9u-eIuVTazSndZPeNcTZA,1066
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+ gwaslab-3.5.0.dist-info/METADATA,sha256=SocHVFBOrjeEchxsvVLUgI4CZPwSypppxfSE7o7yp1I,7751
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+ gwaslab-3.5.0.dist-info/WHEEL,sha256=OVMc5UfuAQiSplgO0_WdW7vXVGAt9Hdd6qtN4HotdyA,91
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+ gwaslab-3.5.0.dist-info/top_level.txt,sha256=PyY6hWtrALpv2MAN3kjkIAzJNmmBTH5a2risz9KwH08,8
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+ gwaslab-3.5.0.dist-info/RECORD,,
{gwaslab-3.4.48.dist-info → gwaslab-3.5.0.dist-info}/WHEEL RENAMED
@@ -1,5 +1,5 @@
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  Wheel-Version: 1.0
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- Generator: setuptools (73.0.1)
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+ Generator: setuptools (75.2.0)
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  Root-Is-Purelib: true
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  Tag: py3-none-any
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