From c3cac235faa4dfbaf6cd14838fc095c9bd369497 Mon Sep 17 00:00:00 2001
From: hjulienn <hanna.julienne@pasteur.fr>
Date: Tue, 22 Feb 2022 17:54:40 +0100
Subject: [PATCH] modify max length allele
---
jass/models/inittable.py | 2 +-
jass/models/worktable.py | 12 ++++++------
2 files changed, 7 insertions(+), 7 deletions(-)
diff --git a/jass/models/inittable.py b/jass/models/inittable.py
index 7a4d2ced..6fbdd8c3 100644
--- a/jass/models/inittable.py
+++ b/jass/models/inittable.py
@@ -265,7 +265,7 @@ def create_inittable_file(
which_cols.extend(list(pheno_select))
hdf_init.put("PhenoList", pheno_list, format="table", data_columns=True)
hdf_init.put("Regions", regions, format="table", data_columns=True)
- sum_stat_tab_min_itemsizes = {"snp_ids": 80, "Ref_allele": 70, "Alt_allele": 70}
+ sum_stat_tab_min_itemsizes = {"snp_ids": 310, "Ref_allele": 300, "Alt_allele": 300}
regions_bychr = regions.groupby("chr")
diff --git a/jass/models/worktable.py b/jass/models/worktable.py
index a67697a0..ee48567c 100644
--- a/jass/models/worktable.py
+++ b/jass/models/worktable.py
@@ -430,20 +430,20 @@ def create_worktable_file(
regions = read_hdf(init_file_path, "Regions").index.tolist()
sum_stat_tab_min_itemsizes = {
- "snp_ids": 80,
+ "snp_ids": 310,
"Region": 10,
"CHR": 5,
- "Ref_allele": 70,
- "Alt_allele": 70,
+ "Ref_allele": 300,
+ "Alt_allele": 300,
}
region_sub_table_min_itemsizes = {
"Region": 10,
"index": 10,
"CHR": 5,
- "snp_ids": 80,
+ "snp_ids": 310,
"signif_status": 20,
- "Ref_allele": 70,
- "Alt_allele": 70,
+ "Ref_allele": 300,
+ "Alt_allele": 300,
}
smart_na_computation = not (remove_nan)
--
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