gwaslab 3.5.3__py3-none-any.whl → 3.5.5__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

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Files changed (26) hide show
  1. gwaslab/__init__.py +2 -1
  2. gwaslab/g_Sumstats.py +29 -8
  3. gwaslab/g_SumstatsPair.py +16 -12
  4. gwaslab/g_headers.py +131 -0
  5. gwaslab/g_meta.py +2 -1
  6. gwaslab/g_version.py +3 -3
  7. gwaslab/io_preformat_input.py +29 -7
  8. gwaslab/io_read_pipcs.py +23 -0
  9. gwaslab/io_to_formats.py +45 -44
  10. gwaslab/qc_check_datatype.py +65 -42
  11. gwaslab/util_ex_ldsc.py +9 -0
  12. gwaslab/util_ex_run_2samplemr.py +34 -0
  13. gwaslab/util_ex_run_clumping.py +4 -2
  14. gwaslab/util_in_fill_data.py +9 -1
  15. gwaslab/util_in_filter_value.py +15 -1
  16. gwaslab/viz_plot_credible_sets.py +99 -0
  17. gwaslab/viz_plot_miamiplot2.py +11 -4
  18. gwaslab/viz_plot_mqqplot.py +14 -11
  19. gwaslab/viz_plot_stackedregional.py +64 -33
  20. {gwaslab-3.5.3.dist-info → gwaslab-3.5.5.dist-info}/METADATA +3 -3
  21. {gwaslab-3.5.3.dist-info → gwaslab-3.5.5.dist-info}/RECORD +25 -23
  22. gwaslab/vis_plot_credible sets.py +0 -0
  23. {gwaslab-3.5.3.dist-info → gwaslab-3.5.5.dist-info}/LICENSE +0 -0
  24. {gwaslab-3.5.3.dist-info → gwaslab-3.5.5.dist-info}/LICENSE_before_v3.4.39 +0 -0
  25. {gwaslab-3.5.3.dist-info → gwaslab-3.5.5.dist-info}/WHEEL +0 -0
  26. {gwaslab-3.5.3.dist-info → gwaslab-3.5.5.dist-info}/top_level.txt +0 -0
{gwaslab-3.5.3.dist-info → gwaslab-3.5.5.dist-info}/RECORD RENAMED
@@ -1,4 +1,4 @@
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- gwaslab/__init__.py,sha256=pP_OQwkaXMJokVVU_o6AXnJEBs2HtaMtpcHIls3ezO8,2486
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+ gwaslab/__init__.py,sha256=wyK0byyNw9vz6bcZDOA8r81-weibcnbNGggx_K6pT7s,2539
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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
@@ -6,21 +6,23 @@ gwaslab/bd_get_hapmap3.py,sha256=FQpwbhWUPFT152QtiLevEkkN4YcVDIeKzoK0Uz1NlRo,410
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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=eqEpHEH5fnBMsOIufVzwaRp0_vCsuHvGEUe5OzNL41s,36969
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- gwaslab/g_SumstatsPair.py,sha256=20snPb4SlI6ftMGVjgxAuyxsxYRQF-GzzlBSnoB-3Lo,8851
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+ gwaslab/g_Sumstats.py,sha256=M85hI9HkyzUV9RqCdIBpoIlD9uA7QDcdlq1M-Fpvv_M,37769
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+ gwaslab/g_SumstatsPair.py,sha256=71fPfwhr9pdH9pdyX17bSEu8ah_WVpTVU0nc_4uln4Y,8766
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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_headers.py,sha256=Q37MZgc2G1bMzzJX94Kq6GoRYJyfUxQX50CvyIerXww,6524
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+ gwaslab/g_meta.py,sha256=Orj8WhFvbylDmaAp9Px_GRUoyEBVML8MLa9829sNM0o,2588
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  gwaslab/g_vchange_status.py,sha256=w3zsYYOcCaI3PTeboonvkQjudzUAfVIgATzRdiPViZs,1939
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- gwaslab/g_version.py,sha256=wfkMhPi1U1fd25HKu8F5F4j1YcnYQslOrERu0bBTD38,1885
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+ gwaslab/g_version.py,sha256=xQqOnBdKHR2JYgA4nuFyJcsmUNx3MbwJg640M-_N40Y,1889
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  gwaslab/hm_casting.py,sha256=FqP4EQl83Q2OKLw004OgLIvUH795TVCGwziLk5jsHqY,11368
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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=J8Ny4OPMaLVdo2nP8lTM-c5A8LSdqphSrp9G4i9JjDQ,24097
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+ gwaslab/io_preformat_input.py,sha256=cfoywijnk1z1QeTMOXL_lqcheI3GA_Ff4uOUNxAqCq4,25331
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  gwaslab/io_process_args.py,sha256=0ljJOVGsD7qPuBLvdfvR7Vrh7zXPlvfPg-rhOw8xRpQ,1366
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  gwaslab/io_read_ldsc.py,sha256=wsYXpH50IchBKd2dhYloSqc4YgnDkiwMsAweaCoN5Eo,12471
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+ gwaslab/io_read_pipcs.py,sha256=17ycVJT1qwx3MBzcRdTlAf_7RiFKGilgoc7eq7kFtog,994
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  gwaslab/io_read_tabular.py,sha256=EG-C6KhCutt4J4LlOMgXnqzJvU-EZXzVhMvaDFnHrMM,2380
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- gwaslab/io_to_formats.py,sha256=hiIaR-JKOVehv7Y14_SklvzPi_E4U-wUybjKWfPyIus,32587
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+ gwaslab/io_to_formats.py,sha256=uAmZ4xzVoJqXGXxwTZlbppli4fPc2EshnuTJm2DC4v8,32799
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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 +30,7 @@ gwaslab/ldsc_ldscore.py,sha256=ZOxMvV3PhZzLsTmkKQqjabk_9PdrCTtPhbrdrpGmRAk,14580
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  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_check_datatype.py,sha256=mAM0LCMf9LseX44oeELG0croPlxfp7U8A8TH-Y5F6kQ,4453
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  gwaslab/qc_fix_sumstats.py,sha256=u0YfC70zop2roUfq6mLMNL49m8AHPF2G-j8dKqW25yY,98261
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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
@@ -36,25 +38,24 @@ gwaslab/util_ex_calculate_ldmatrix.py,sha256=Z_spxbq6SHDS0v84I59YTTF40iyLQIOZbt0
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  gwaslab/util_ex_calculate_prs.py,sha256=9uJ588Sdj4V0vw3OZ9NeLECwOvW67f0IdLandVPS5RY,9442
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  gwaslab/util_ex_gwascatalog.py,sha256=--Gde9HrsikfYTeFqSaYz0gUODr9wmv_gV6GZGNlElg,7688
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  gwaslab/util_ex_ldproxyfinder.py,sha256=wWNW9wITWozj23gT41LR00WxU-rrHpGKbxs2H_3jEyM,9431
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- gwaslab/util_ex_ldsc.py,sha256=dd3QUNX7eOJY_z4mkKIE9Ey_SQGE4ox0efhq28ah_LE,18592
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+ gwaslab/util_ex_ldsc.py,sha256=dMfL7hej0JzTOafPk6VYl5HUxB3eSp28wUKVWliIhlE,18937
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  gwaslab/util_ex_plink_filter.py,sha256=pK1Yxtv9-J4rMOdVAG7VU9PktvI6-y4FxBiVEH0QuRs,1673
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  gwaslab/util_ex_process_h5.py,sha256=ynFvo3zxgvOxWYL565v2IQf8P6iEuq7UlKQ_ULxrd6Y,2831
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  gwaslab/util_ex_process_ref.py,sha256=GQ0ZEWLxGpHLdBs3tqnAqKn3Pqx1A1YvNbYrBLBvXeg,17126
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- gwaslab/util_ex_run_2samplemr.py,sha256=5c0DGF694T9j0Y58L2I7pr1_Z1hfpaatIgix7P5oPA8,9127
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- gwaslab/util_ex_run_clumping.py,sha256=bs9CJENMhwVXolCNygaYtso5ikPrdPMiV13tGA0ttxg,7915
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+ gwaslab/util_ex_run_2samplemr.py,sha256=wBr5s0XKlzqLe5ZyskvpeWUv-0fgnynBk0DCfnax-sc,10429
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+ gwaslab/util_ex_run_clumping.py,sha256=yvUhKi83KhXfE5yPy2i47B58BMACZ_r5gt3-uN8Znbo,7908
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  gwaslab/util_ex_run_coloc.py,sha256=u57h8wPbTCOf6aY5u5DpzK1gv7inuDT8a15UGo-1ras,6288
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  gwaslab/util_ex_run_susie.py,sha256=TXqiwBVq1io7XSlLF2_gNsYgxDLiKNnYE9pIjRWJ1Hc,5315
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  gwaslab/util_in_calculate_gc.py,sha256=MWOXVzJv7SZx4i2_ncRiqsiEOADc7EfghaUzgGy4jaE,2219
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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=iVq5WLWwFI03v9HyvBanu5si3j2p-oyPFTl8jsX69xM,14693
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- gwaslab/util_in_filter_value.py,sha256=dY4X66N9A4MHCRHjPqLYFufMM91ggLRwUBf_nJYh8Lg,23605
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+ gwaslab/util_in_fill_data.py,sha256=wQwx3vtN1gJzJKc_FUZRk5xLLza1OeUa90z7d9G1Iis,14934
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+ gwaslab/util_in_filter_value.py,sha256=DXAjIei9OkD-4C3CSkMEu-9vwVB5-vvLP4wospzlDEE,24252
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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=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/vis_plot_credible sets.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  gwaslab/viz_aux_annotate_plot.py,sha256=3PyBioC-3ZBzqKT2JRv6vp-hZUXSqTTePIT5cblEvnQ,25334
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  gwaslab/viz_aux_chromatin.py,sha256=aWZaXOSvGyZY7wQcoFDaqHRYCSHZbi_K4Q70HruN9ts,4125
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  gwaslab/viz_aux_property.py,sha256=UIaivghnLXYpTwkKnXRK0F28Jbn9L6OaICk3K73WZaU,33
@@ -63,17 +64,18 @@ gwaslab/viz_aux_reposition_text.py,sha256=iRIP-Rkltlei068HekJcVubiqPrunBqvAoSQ1e
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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=kq-rVWygHEeTBMOtd_jk8nK85ClZHU-ADSf4nI2gTKo,66604
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+ gwaslab/viz_plot_credible_sets.py,sha256=KxB7_bkDrLMgs6sk8HAnZWkllIRH-lEDCz5n5_Jnw68,3550
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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=xiFCgFX8hEySmCJORpEurMVER9eEXQyy_Ik7mLkbi9g,16015
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- gwaslab/viz_plot_mqqplot.py,sha256=Pea0uNWe4ZW3S8z8BGQ_dIEWmnKWoxAgEMVxGsMJYxk,68560
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+ gwaslab/viz_plot_miamiplot2.py,sha256=nA8xAI0ou3rBobm3DygOQSpunhZWwXVilKVd0v4Jfac,16213
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+ gwaslab/viz_plot_mqqplot.py,sha256=AdEqATd6kpdwP_rQbwDIP6usJG3OUOSzfr43h3TKpmM,68710
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  gwaslab/viz_plot_regional2.py,sha256=rvvIU60pOJFiDReQFd_Q2MkthuwvNOUkptV1swP9uJM,39444
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  gwaslab/viz_plot_rg_heatmap.py,sha256=PidUsgOiEVt6MfBPCF3_yDhOEytZ-I1q-ZD6_0pFrV4,13713
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  gwaslab/viz_plot_scatter_with_reg.py,sha256=PmUZDQl2q4Dme3HLPXEwf_TrMjwJADA-uFXNDBWUEa4,8333
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- gwaslab/viz_plot_stackedregional.py,sha256=UefPxnd-EJApFdwcafE2k6jZqrfGKEjy51NhieiRaPM,17362
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+ gwaslab/viz_plot_stackedregional.py,sha256=WckcESSIHQuRCN37cnjzWLWiHCrQT3kUVkRCFiq2bk8,18614
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@@ -83,9 +85,9 @@ gwaslab/data/hapmap3_SNPs/hapmap3_db150_hg19.snplist.gz,sha256=qD9RsC5S2h6l-OdpW
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- gwaslab-3.5.3.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
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- gwaslab-3.5.3.dist-info/LICENSE_before_v3.4.39,sha256=GhLOU_1UDEKeOacYhsRN_m9u-eIuVTazSndZPeNcTZA,1066
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- gwaslab-3.5.3.dist-info/METADATA,sha256=lMetRGVrgpM2KaxU-y17WKZhZkOd7aafJY1pta3oKJA,7758
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- gwaslab-3.5.3.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
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- gwaslab-3.5.3.dist-info/top_level.txt,sha256=PyY6hWtrALpv2MAN3kjkIAzJNmmBTH5a2risz9KwH08,8
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- gwaslab-3.5.3.dist-info/RECORD,,
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+ gwaslab-3.5.5.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
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+ gwaslab-3.5.5.dist-info/LICENSE_before_v3.4.39,sha256=GhLOU_1UDEKeOacYhsRN_m9u-eIuVTazSndZPeNcTZA,1066
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+ gwaslab-3.5.5.dist-info/METADATA,sha256=BAkr3vpGpZJqHRecRn_q4guTT8PeykLZssU02mL1T7Q,7750
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+ gwaslab-3.5.5.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
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+ gwaslab-3.5.5.dist-info/top_level.txt,sha256=PyY6hWtrALpv2MAN3kjkIAzJNmmBTH5a2risz9KwH08,8
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+ gwaslab-3.5.5.dist-info/RECORD,,
gwaslab/vis_plot_credible sets.py DELETED
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