count_control file gives same output regardless of arguments or input types

[Kaskere]

Hello,
I tested count_controls.py using different population parameters ( pop --FIN, pop --NFE, --ALL), and also with gnomad controls, where all women controls were removed. Resulting snp file was equal in all cases. I suggest count_controls.py needs to be debugged.

detailed explanation:

usr$ tail fileFIN.txt
ENSG00000134709 14588 0 14588
ENSG00000144339 3208 0 3208
ENSG00000134258 15556 0 15556
ENSG00000213999 49990 0 49990
ENSG00000124935 52094 0 52094
ENSG00000256757 82256 0 82256
ENSG00000161217 317597 0 317597
ENSG00000256206 0 0 0
ENSG00000287856 88429 0 88429
ENSG00000256751 135949 0 135949
usr$ tail fileASJ.txt
ENSG00000134709 14588 0 14588
ENSG00000144339 3208 0 3208
ENSG00000134258 15556 0 15556
ENSG00000213999 49990 0 49990
ENSG00000124935 52094 0 52094
ENSG00000256757 82256 0 82256
ENSG00000161217 317597 0 317597
ENSG00000256206 0 0 0
ENSG00000287856 88429 0 88429
ENSG00000256751 135949 0 135949

the usage was as follows:
python2.7 --pop ASJ count_controls.py -v gnomad.gz -s makesnp.txt -o out

gnomad controls were downloaded as separate file for each chromosome and prepared as follows:

1. extracted exome regions with bcftools view
2. normalised with bcftools normalise
3. filtered by MAF, DP, quality
4. resulting chromosome files concatenated