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-rw-r--r--wqflask/wqflask/marker_regression/gemma_mapping.py6
1 files changed, 1 insertions, 5 deletions
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 769688ff..11feaa98 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -71,11 +71,7 @@ def run_gemma(this_dataset, samples, vals, covariates, use_loco, maf=0.01):
gwa_output_filename)
else:
-<<<<<<< HEAD
- gemma_command = GEMMA_COMMAND + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -k %s/%s.cXX.txt -lmm 2 -maf %s' % (flat_files('genotype/bimbam'),
-=======
- gemma_command = GEMMA_COMMAND + ' ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -k %s/%s.cXX.txt -lmm 2 -maf 0.1' % (flat_files('genotype/bimbam'),
->>>>>>> b2a7886df64073042a89b466cc103f9bbf06827a
+ gemma_command = GEMMA_COMMAND + ' ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -k %s/%s.cXX.txt -lmm 2 -maf %s' % (flat_files('genotype/bimbam'),
genofile_name,
flat_files('genotype/bimbam'),
genofile_name,