Add ability to read pgen genotype format

CMakeLists.txt

@@ -37,6 +37,16 @@ target_include_directories(quasar PRIVATE ${EXTERN_LIBS_PATH}/cxxopts/include/)
 target_include_directories(quasar PRIVATE ${EXTERN_LIBS_PATH}/eigen-3.4.0/)
 target_include_directories(quasar PRIVATE ${EXTERN_LIBS_PATH}/brent/)
 
+set(PGEN_PATH "${EXTERN_LIBS_PATH}/pgenlib")
+add_custom_target(
+   pgenlib
+   COMMAND make
+   WORKING_DIRECTORY ${PGEN_PATH}
+)
+target_link_libraries(quasar PRIVATE ${PGEN_PATH}/pgenlib.a)
+target_include_directories(quasar PRIVATE ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/)
+add_dependencies(quasar pgenlib)
+
 enable_testing()
 
 add_executable(quasar_tests EXCLUDE_FROM_ALL tests/test_smoke.cpp)

example/chr22-n100.psam

@@ -0,0 +1,101 @@
+#IID	SEX
+691_692	NA
+693_694	NA
+688_689	NA
+683_684	NA
+684_685	NA
+686_687	NA
+689_690	NA
+687_688	NA
+690_691	NA
+685_686	NA
+692_693	NA
+682_683	NA
+825_826	NA
+823_824	NA
+829_830	NA
+832_833	NA
+831_832	NA
+827_828	NA
+830_831	NA
+824_825	NA
+842_843	NA
+843_844	NA
+826_827	NA
+847_848	NA
+836_837	NA
+990_991	NA
+835_836	NA
+848_849	NA
+989_990	NA
+997_998	NA
+834_835	NA
+849_850	NA
+985_986	NA
+851_852	NA
+845_846	NA
+850_851	NA
+846_847	NA
+852_853	NA
+999_1000	NA
+996_997	NA
+995_996	NA
+812_813	NA
+994_995	NA
+991_992	NA
+992_993	NA
+998_999	NA
+811_812	NA
+810_811	NA
+986_987	NA
+993_994	NA
+857_858	NA
+1003_1004	NA
+1002_1003	NA
+854_855	NA
+855_856	NA
+1004_1005	NA
+858_859	NA
+1000_1001	NA
+1001_1002	NA
+987_988	NA
+856_857	NA
+853_854	NA
+988_989	NA
+859_860	NA
+802_803	NA
+804_805	NA
+891_892	NA
+865_866	NA
+1007_1008	NA
+861_862	NA
+862_863	NA
+860_861	NA
+864_865	NA
+1006_1007	NA
+803_804	NA
+863_864	NA
+890_891	NA
+1005_1006	NA
+1009_1010	NA
+805_806	NA
+1010_1011	NA
+1008_1009	NA
+807_808	NA
+893_894	NA
+806_807	NA
+892_893	NA
+1011_1012	NA
+1014_1015	NA
+808_809	NA
+809_810	NA
+1012_1013	NA
+1021_1022	NA
+1016_1017	NA
+1023_1024	NA
+1018_1019	NA
+898_899	NA
+1019_1020	NA
+894_895	NA
+899_900	NA
+896_897	NA