From 46ff85c7b6eed932ab248cec0abaf654a74cb43d Mon Sep 17 00:00:00 2001
From: Hanna JULIENNE <hanna.julienne@pasteur.fr>
Date: Thu, 3 Feb 2022 16:52:52 +0100
Subject: [PATCH] Update __main__.py Remove --index-type argument the index
type is specified in the meta data file describing the study
---
jass_preprocessing/__main__.py | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/jass_preprocessing/__main__.py b/jass_preprocessing/__main__.py
index 75e3880..b089d3c 100644
--- a/jass_preprocessing/__main__.py
+++ b/jass_preprocessing/__main__.py
@@ -2,7 +2,7 @@
Read raw GWAS summary statistics, filter and format
Write clean GWAS datasets by chromosome
"""
-__updated__ = '2018-26-06'
+__updated__ = '2022-03-02'
import pandas as pd
import jass_preprocessing as jp
@@ -95,7 +95,6 @@ def add_preprocessing_argument():
parser.add_argument('--additional-masked-region', required=False, help= "List of dictionary containing coordinate of region to mask. For example :[{'chr':6, 'start':50000000, 'end': 70000000}, {'chr':6, 'start':100000000, 'end': 120000000}]", default='None')
parser.add_argument('--imputation-quality-treshold', required=False, help= "minimum imputation quality in summary statistics", default='None')
- parser.add_argument('--index-type', required=False, help= "type of index : rsID or chr:postion:ref_allele:alt_allele", default='rs-number')
parser.set_defaults(func=launch_preprocessing)
--
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