pixy doesnt handle masked haplotype data?

[jamesfifer]

Hello, thanks for making such a useful tool!

I am trying to run pixy to calculate pi on a masked vcf file that will often have one haplotype masked (i.e. marked as missing) while the other haplotype has genotype data (i.e. 1 or 0). I dont get any errors when running pixy but the output will always have "NA" because it thinks all pairwise comps contain missing data. Output will look like:

pop chromosome window_pos_1 window_pos_2 avg_pi no_sites count_diffs count_comparisons count_missing
Ngoye NC_035107.1 379329 399328 NA 0 0 0 8265
Angola NC_035107.1 379329 399328 NA 0 0 0 6175

I am running:
for chr in {1..3}; do
pixy --stats pi fst dxy
--vcf chr${chr}_Angola_Ngoye.2hap.vcf.gz
--populations Ngoye.Angola.samplemap
--n_cores 4
--bed_file chr${chr}_Angola_Ngoye.2hap_20k.bed
--output_prefix chr${chr}_Angola_Ngoye.2hap --bypass_invariant_check yes; done

my vcf file looks like:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Debug010_aegypti_Cuanda_Angola_02 Debug010_aegypti_Cuanda_Angola_05 Debug010_aegypti_Cuanda_Angola_06 Debug010_aegypti_Cuanda_Angola_08 Debug010_aegypti_Cuanda_Angola_09 Debug010_aegypti_Cuanda_Angola_10 Debug010_aegypti_Cuanda_Angola_11 Debug010_aegypti_Cuanda_Angola_12 Debug010_aegypti_Cuanda_Angola_14 Debug010_aegypti_Cuanda_Angola_16 Debug010_aegypti_Cuanda_Angola_17 Debug010_aegypti_Cuanda_Angola_19 Debug010_aegypti_Cuanda_Angola_20 Debug024_aegypti_Ngoye_Senegal_F_10 Debug024_aegypti_Ngoye_Senegal_F_11 Debug024_aegypti_Ngoye_Senegal_F_12 Debug024_aegypti_Ngoye_Senegal_F_16 Debug024_aegypti_Ngoye_Senegal_F_1 Debug024_aegypti_Ngoye_Senegal_F_20 Debug024_aegypti_Ngoye_Senegal_F_3 Debug024_aegypti_Ngoye_Senegal_F_8 Debug024_aegypti_Ngoye_Senegal_M_13 Debug024_aegypti_Ngoye_Senegal_M_14 Debug024_aegypti_Ngoye_Senegal_M_15 Debug024_aegypti_Ngoye_Senegal_M_17 Debug024_aegypti_Ngoye_Senegal_M_18 Debug024_aegypti_Ngoye_Senegal_M_6 Debug024_aegypti_Ngoye_Senegal_M_9
NC_035107.1 379329 . C T . . AF=0.0706806;CM=0.209779;AN=23;AC=13 GT ./. ./. ./. 1/. ./. ./. 0/. ./. ./../. ./. 0/. ./. 0|1 1/. 0|1 1|1 1|0 .|1 ./. 1|1 ./. ./. 0|1 1|0 0|0 1|0 ./.

Bed file:
NC_035107.1 379329 399328

Pops file:
Debug024_aegypti_Ngoye_Senegal_F_10 Ngoye
Debug024_aegypti_Ngoye_Senegal_F_11 Ngoye
Debug024_aegypti_Ngoye_Senegal_F_12 Ngoye
Debug024_aegypti_Ngoye_Senegal_F_16 Ngoye
Debug024_aegypti_Ngoye_Senegal_F_1 Ngoye
Debug024_aegypti_Ngoye_Senegal_F_20 Ngoye
Debug024_aegypti_Ngoye_Senegal_F_3 Ngoye
Debug024_aegypti_Ngoye_Senegal_F_8 Ngoye
Debug024_aegypti_Ngoye_Senegal_M_13 Ngoye
Debug024_aegypti_Ngoye_Senegal_M_14 Ngoye
Debug024_aegypti_Ngoye_Senegal_M_15 Ngoye
Debug024_aegypti_Ngoye_Senegal_M_17 Ngoye
Debug024_aegypti_Ngoye_Senegal_M_18 Ngoye
Debug024_aegypti_Ngoye_Senegal_M_6 Ngoye
Debug024_aegypti_Ngoye_Senegal_M_9 Ngoye
Debug010_aegypti_Cuanda_Angola_02 Angola
Debug010_aegypti_Cuanda_Angola_05 Angola
Debug010_aegypti_Cuanda_Angola_06 Angola
Debug010_aegypti_Cuanda_Angola_08 Angola
Debug010_aegypti_Cuanda_Angola_09 Angola
Debug010_aegypti_Cuanda_Angola_10 Angola
Debug010_aegypti_Cuanda_Angola_11 Angola
Debug010_aegypti_Cuanda_Angola_12 Angola
Debug010_aegypti_Cuanda_Angola_14 Angola
Debug010_aegypti_Cuanda_Angola_16 Angola
Debug010_aegypti_Cuanda_Angola_17 Angola
Debug010_aegypti_Cuanda_Angola_19 Angola
Debug010_aegypti_Cuanda_Angola_20 Angola