├── .gitignore ├── LICENSE ├── Makefile ├── README.md ├── scripts ├── b2d ├── calpha.py ├── calpha_perm.py ├── d2b ├── d2h ├── fill_m.py ├── h2d ├── indi2indu ├── macs_hap_to_vcf.py ├── pca.py ├── pca_dark.py ├── pca_light.py └── simple_ped.sh ├── src ├── Makefile ├── bcf.c ├── bcf.h ├── bim.c ├── bim.h ├── convert.c ├── count.c ├── genotq.c ├── genotq.h ├── gqt.c ├── gt.c ├── ihs.c ├── misc.c ├── off.c ├── off.h ├── output_buffer.c ├── output_buffer.h ├── parse_q.c ├── parse_q.h ├── parse_q.l ├── ped.c ├── ped.h ├── plt.c ├── plt.h ├── pop.c ├── pq.c ├── pq.h ├── pthread_pool.c ├── pthread_pool.h ├── query.c ├── quick_file.c ├── quick_file.h ├── read_binary_uints.c ├── sandbox.c ├── sort.c ├── sum.c ├── timer.c ├── timer.h ├── ubin.c ├── ubin.h ├── vari_to_varub.c ├── vcf_to_plt.c ├── vid.c ├── vid.h ├── view.c ├── wah.c ├── wah.h ├── wahbm.c ├── wahbm.h ├── wahbm_compressed_in_place.c ├── wahbm_compressed_in_place.h ├── wahbm_in_place.c └── wahbm_in_place.h └── test ├── data ├── 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