From 261ba5e41408d212cc3c33df658b6be2431f68ad Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 11 Oct 2018 15:43:41 +0000
Subject: - Added fix for GEMMA LOCO

- Added all current SNP browser code (not complete yet)

- Added change to convert_geno_to_bimbam that makes it ignore .geno files marked as "filler" (so ones where the .geno file is fake and we sometimes directly receive the genotypes as BIMBAM)

- Changes TheSpecies object in species.py to accept species name as well as dataset name
---
 wqflask/maintenance/convert_geno_to_bimbam.py | 2 ++
 1 file changed, 2 insertions(+)

(limited to 'wqflask/maintenance')

diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py
index a5d2d12a..8f331a06 100644
--- a/wqflask/maintenance/convert_geno_to_bimbam.py
+++ b/wqflask/maintenance/convert_geno_to_bimbam.py
@@ -140,6 +140,8 @@ class ConvertGenoFile(object):
                 key, _separater, value = row.partition(':')
                 key = key.strip()
                 value = value.strip()
+                if key == "@filler":
+                    raise EmptyConfigurations
                 if key in self.haplotype_notation:
                     self.configurations[value] = self.haplotype_notation[key]
                 continue
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