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opticall committed 0a330a3

opticall version 0.3.0, more features, including outlier removal, and a little quicker

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Files changed (9)

opticall/Makefile

-opticall: opticall.o kmpp/KMeans.o kmpp/KmTree.o kmpp/KmUtils.o 
-	g++ -m64 -o opticall opticall.o kmpp/KMeans.o kmpp/KmTree.o kmpp/KmUtils.o
+opticall: opticall.o filtering.o kmpp/KMeans.o kmpp/KmTree.o kmpp/KmUtils.o 
+	g++ -m64 -o opticall opticall.o filtering.o kmpp/KMeans.o kmpp/KmTree.o kmpp/KmUtils.o
 	rm *.o
 	rm kmpp/*.o
 
-opticall.o: opticall.cpp 
+opticall.o: opticall.cpp inclusions.h filtering.h
 	g++ -m64 -I libs -I libs/eigen -c opticall.cpp	
 
+
+filtering.o: filtering.cpp inclusions.h
+	g++ -m64 -I libs -I libs/eigen -c filtering.cpp
+
+
 kmpp/KMeans.o: kmpp/KMeans.cpp kmpp/KMeans.h kmpp/KmTree.h
 	g++ -m64 -c kmpp/KMeans.cpp -o kmpp/KMeans.o
 

opticall/example.int

+SNP	Coor	Alleles	sample1_A	sample1_B	sample2_A	sample2_B	sample3_A	sample3_B	sample4_A	sample4_B	sample5_A	sample5_B	sample6_A	sample6_B	sample7_A	sample7_B	sample8_A	sample8_B	sample9_A	sample9_B	sample10_A	sample10_B	sample11_A	sample11_B	sample12_A	sample12_B	sample13_A	sample13_B	sample14_A	sample14_B	sample15_A	sample15_B	sample16_A	sample16_B	sample17_A	sample17_B	sample18_A	sample18_B	sample19_A	sample19_B	sample20_A	sample20_B	sample21_A	sample21_B	sample22_A	sample22_B	sample23_A	sample23_B	sample24_A	sample24_B	sample25_A	sample25_B	sample26_A	sample26_B	sample27_A	sample27_B	sample28_A	sample28_B	sample29_A	sample29_B	sample30_A	sample30_B	sample31_A	sample31_B	sample32_A	sample32_B	sample33_A	sample33_B	sample34_A	sample34_B	sample35_A	sample35_B	sample36_A	sample36_B	sample37_A	sample37_B	sample38_A	sample38_B	sample39_A	sample39_B	sample40_A	sample40_B	sample41_A	sample41_B	sample42_A	sample42_B	sample43_A	sample43_B	sample44_A	sample44_B	sample45_A	sample45_B	sample46_A	sample46_B	sample47_A	sample47_B	sample48_A	sample48_B	sample49_A	sample49_B	sample50_A	sample50_B	sample51_A	sample51_B	sample52_A	sample52_B	sample53_A	sample53_B	sample54_A	sample54_B	sample55_A	sample55_B	sample56_A	sample56_B	sample57_A	sample57_B	sample58_A	sample58_B	sample59_A	sample59_B	sample60_A	sample60_B	sample61_A	sample61_B	sample62_A	sample62_B	sample63_A	sample63_B	sample64_A	sample64_B	sample65_A	sample65_B	sample66_A	sample66_B	sample67_A	sample67_B	sample68_A	sample68_B	sample69_A	sample69_B	sample70_A	sample70_B	sample71_A	sample71_B	sample72_A	sample72_B	sample73_A	sample73_B	sample74_A	sample74_B	sample75_A	sample75_B	sample76_A	sample76_B	sample77_A	sample77_B	sample78_A	sample78_B	sample79_A	sample79_B	sample80_A	sample80_B	sample81_A	sample81_B	sample82_A	sample82_B	sample83_A	sample83_B	sample84_A	sample84_B	sample85_A	sample85_B	sample86_A	sample86_B	sample87_A	sample87_B	sample88_A	sample88_B	sample89_A	sample89_B	sample90_A	sample90_B	sample91_A	sample91_B	sample92_A	sample92_B	sample93_A	sample93_B	sample94_A	sample94_B	sample95_A	sample95_B	sample96_A	sample96_B	sample97_A	sample97_B	sample98_A	sample98_B	sample99_A	sample99_B	sample100_A	sample100_B	sample101_A	sample101_B	sample102_A	sample102_B	sample103_A	sample103_B	sample104_A	sample104_B	sample105_A	sample105_B	sample106_A	sample106_B	sample107_A	sample107_B	sample108_A	sample108_B	sample109_A	sample109_B	sample110_A	sample110_B	sample111_A	sample111_B	sample112_A	sample112_B	sample113_A	sample113_B	sample114_A	sample114_B	sample115_A	sample115_B	sample116_A	sample116_B	sample117_A	sample117_B	sample118_A	sample118_B	sample119_A	sample119_B	sample120_A	sample120_B	sample121_A	sample121_B	sample122_A	sample122_B	sample123_A	sample123_B	sample124_A	sample124_B	sample125_A	sample125_B	sample126_A	sample126_B	sample127_A	sample127_B	sample128_A	sample128_B	sample129_A	sample129_B	sample130_A	sample130_B	sample131_A	sample131_B	sample132_A	sample132_B	sample133_A	sample133_B	sample134_A	sample134_B	sample135_A	sample135_B	sample136_A	sample136_B	sample137_A	sample137_B	sample138_A	sample138_B	sample139_A	sample139_B	sample140_A	sample140_B	sample141_A	sample141_B	sample142_A	sample142_B	sample143_A	sample143_B	sample144_A	sample144_B	sample145_A	sample145_B	sample146_A	sample146_B	sample147_A	sample147_B	sample148_A	sample148_B	sample149_A	sample149_B	sample150_A	sample150_B	sample151_A	sample151_B	sample152_A	sample152_B	sample153_A	sample153_B	sample154_A	sample154_B	sample155_A	sample155_B	sample156_A	sample156_B	sample157_A	sample157_B	sample158_A	sample158_B	sample159_A	sample159_B	sample160_A	sample160_B	sample161_A	sample161_B	sample162_A	sample162_B	sample163_A	sample163_B	sample164_A	sample164_B	sample165_A	sample165_B	sample166_A	sample166_B	sample167_A	sample167_B	sample168_A	sample168_B	sample169_A	sample169_B	sample170_A	sample170_B	sample171_A	sample171_B	sample172_A	sample172_B	sample173_A	sample173_B	sample174_A	sample174_B	sample175_A	sample175_B	sample176_A	sample176_B	sample177_A	sample177_B	sample178_A	sample178_B	sample179_A	sample179_B	sample180_A	sample180_B	sample181_A	sample181_B	sample182_A	sample182_B	sample183_A	sample183_B	sample184_A	sample184_B	sample185_A	sample185_B	sample186_A	sample186_B	sample187_A	sample187_B	sample188_A	sample188_B	sample189_A	sample189_B	sample190_A	sample190_B	sample191_A	sample191_B	sample192_A	sample192_B	sample193_A	sample193_B	sample194_A	sample194_B	sample195_A	sample195_B	sample196_A	sample196_B	sample197_A	sample197_B	sample198_A	sample198_B	sample199_A	sample199_B	sample200_A	sample200_B	sample201_A	sample201_B	sample202_A	sample202_B	sample203_A	sample203_B	sample204_A	sample204_B	sample205_A	sample205_B	sample206_A	sample206_B	sample207_A	sample207_B	sample208_A	sample208_B	sample209_A	sample209_B	sample210_A	sample210_B	sample211_A	sample211_B	sample212_A	sample212_B	sample213_A	sample213_B	sample214_A	sample214_B	sample215_A	sample215_B	sample216_A	sample216_B	sample217_A	sa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1	0.944	0.011	0.859	0.028	0.847	0.029	0.929	0.026	0.799	0.036	0.873	0.024	0.916	0.034	0.970	0.031	0.905	0.015	0.904	0.041	0.851	0.038	0.982	0.455	0.634	0.036	0.945	0.414	0.601	0.435	0.679	0.031	0.938	0.041	0.868	0.031	1.008	0.031	0.988	0.020	0.896	0.438	0.643	0.018	0.913	0.030	0.950	0.017	0.737	0.023	0.921	0.301	0.460	0.019	0.919	0.041	0.923	0.042	0.889	0.528	0.644	0.028	1.038	0.027	0.973	0.020	0.958	0.028	1.015	0.052	0.923	0.021	0.981	0.037	0.951	0.465	0.626	0.023	0.932	0.023	0.975	0.021	0.922	0.032	0.850	0.027	1.026	0.040	1.059	0.039	0.966	0.034	0.981	0.037	0.995	0.488	0.664	0.034	1.026	0.024	0.910	0.025	0.822	0.042	0.894	0.028	0.931	0.034	1.034	0.033	0.927	0.424	0.669	0.023	0.913	0.034	1.036	0.021	0.745	0.399	0.587	0.437	0.634	0.034	0.813	0.038	0.827	0.042	0.980	0.038	0.989	0.030	0.936	0.027	0.981	0.030	0.953	0.415	0.640	0.044	0.904	0.360	0.548	0.440	0.628	0.047	0.940	0.029	1.080	0.025	0.891	0.025	0.937	0.018	0.881	0.417	0.664	0.472	0.699	0.048	0.916	0.029	0.900	0.016	0.959	0.019	0.928	0.047	1.076	0.034	0.887	0.030	0.907	0.023	0.947	0.477	0.614	0.030	1.001	0.022	0.862	0.411	0.648	0.025	0.849	0.034	0.846	0.050	0.959	0.021	0.998	0.405	0.565	0.047	0.805	0.033	0.944	0.023	0.909	0.025	0.823	0.032	0.912	0.030	0.979	0.022	1.038	0.039	0.931	0.031	0.872	0.025	0.944	0.033	0.995	0.029	0.867	0.022	0.852	0.445	0.689	0.051	0.953	0.024	1.031	0.431	0.639	0.013	0.929	0.035	0.964	0.029	0.958	0.016	0.885	0.035	0.849	0.387	0.642	0.032	0.994	0.017	1.054	0.016	0.867	0.017	0.862	0.019	0.940	0.031	0.897	0.030	0.872	0.517	0.653	0.039	0.891	0.027	0.935	0.020	0.912	0.025	0.744	0.025	0.855	0.021	0.901	0.049	0.928	0.438	0.676	0.030	0.932	0.023	0.902	0.030	0.936	0.038	0.902	0.453	0.669	0.026	0.879	0.018	1.017	0.036	0.905	0.032	0.893	0.486	0.736	0.031	0.953	0.026	0.911	0.017	0.863	0.022	0.942	0.032	0.912	0.023	0.901	0.060	1.010	0.026	0.934	0.023	0.889	0.021	0.939	0.030	0.958	0.028	1.004	0.033	0.930	0.009	0.915	0.408	0.612	0.029	0.983	0.033	0.952	0.046	0.925	0.476	0.643	0.035	0.985	0.025	0.954	0.027	0.868
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2	0.835	0.057	1.172	0.114	1.138	0.729	0.846	0.598	0.894	0.624	0.839	0.131	1.230	0.119	1.226	0.712	0.848	0.152	1.109	0.053	1.226	0.107	1.213	0.149	1.259	0.145	1.149	0.748	0.900	0.102	1.230	0.129	1.150	0.049	1.166	0.677	0.863	0.136	1.146	0.655	0.870	0.165	1.208	0.122	1.244	0.713	0.865	0.047	1.261	0.152	1.163	0.585	0.795	0.691	0.828	0.145	1.329	0.170	1.232	0.678	0.883	0.107	1.324	0.086	1.118	0.722	0.851	0.123	1.135	0.685	0.844	0.094	1.273	0.111	1.165	0.103	1.232	0.101	1.222	1.073	0.062	0.742	0.848	0.117	1.239	0.138	1.182	0.136	1.221	0.117	1.154	0.729	0.928	0.140	1.256	0.116	1.161	0.128	1.267	0.131	1.233	0.731	0.870	0.131	1.263	0.625	0.875	0.081	1.068	0.118	1.283	0.051	1.223	0.154	1.188	0.676	0.874	0.057	1.165	0.141	1.035	0.676	0.945	0.056	1.260	0.983	0.036	0.665	0.803	0.108	1.048	0.138	1.186	0.633	0.837	0.142	1.241	0.099	1.184	0.704	0.847	0.068	1.134	1.031	0.067	0.666	0.857	0.129	1.195	0.133	1.205	0.115	1.162	0.122	1.192	0.094	1.149	0.119	1.249	0.154	1.199	0.688	0.851	0.145	1.186	0.084	1.330	0.119	1.158	0.125	1.228	0.138	1.247	0.134	1.031	0.143	1.278	0.676	0.930	0.127	1.192	0.109	1.271	0.704	0.848	0.139	1.126	0.652	0.756	0.149	1.154	0.686	0.816	0.075	1.196	0.100	1.249	0.747	0.919	0.044	1.208	0.143	1.164	0.158	1.287	0.056	1.110	0.143	1.246	0.701	0.856	0.649	0.818	0.750	0.908	0.595	0.726	0.527	0.737	0.110	1.333	0.138	1.138	0.124	1.228	0.123	1.169	0.097	1.226	1.100	0.074	0.738	0.857	0.141	1.181	0.652	0.821	0.113	1.202	0.148	1.166	0.761	0.983	0.100	1.154	0.674	0.829	0.735	0.881	0.704	0.808	0.094	1.327	0.142	1.219	0.136	1.268	0.112	1.223	0.130	1.114	0.650	0.825	0.115	1.167	0.596	0.874	0.684	0.813	0.120	1.216	0.131	1.194	0.134	1.283	0.136	1.169	1.076	0.077	0.122	1.206	0.706	0.904	0.098	1.146	0.700	0.825	0.140	1.116	0.139	1.111	0.119	1.128	0.160	1.196	0.149	1.140	0.680	0.872	0.129	1.189	0.092	1.292	0.678	0.849	0.608	0.809	0.756	0.866	0.138	1.208	0.101	1.191	0.703	0.861	0.049	1.229	0.596	0.864	0.122	1.163	0.669	0.822	0.671	0.850	0.580	0.760	1.049	0.082	0.703	0.806	0.690	0.870	0.187	1.194
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3	0.896	0.000	1.235	0.841	0.899	0.013	1.349	0.864	0.792	0.791	0.883	0.001	1.303	0.788	0.944	0.015	1.233	0.009	1.347	0.003	1.249	0.736	0.832	1.271	0.019	0.845	0.852	0.012	1.347	0.011	1.342	0.001	1.266	0.008	1.362	0.778	0.859	0.932	0.831	0.005	1.017	0.009	1.341	0.004	1.290	0.013	1.245	0.011	1.325	0.009	1.342	0.000	1.192	0.741	0.909	0.016	1.377	0.868	0.913	0.004	1.361	0.006	0.929	0.010	1.335	0.819	0.900	0.016	1.293	0.000	1.337	0.010	1.249	0.010	1.259	0.006	1.273	0.005	1.267	0.019	1.217	0.833	0.825	0.007	1.321	0.023	1.396	0.021	1.306	0.011	1.260	0.002	1.367	0.837	0.958	0.010	1.336	0.011	1.264	0.013	1.373	0.786	0.841	0.809	0.919	0.009	1.359	0.001	1.200	0.000	1.347	0.014	1.288	0.004	1.495	0.007	1.206	0.722	0.773	0.001	1.437	0.657	0.745	0.871	0.855	0.756	0.821	0.926	1.016	0.762	0.833	0.009	1.255	0.844	0.897	0.855	0.968	0.763	0.938	0.818	0.867	0.000	1.358	0.683	0.867	0.008	1.383	0.006	1.276	0.004	1.272	0.785	0.899	0.689	0.942	0.004	1.320	0.008	1.325	0.006	1.277	0.005	1.358	0.004	1.216	0.017	1.457	0.771	0.905	0.002	1.219	0.019	1.358	0.000	1.279	0.009	1.219	0.039	0.032	0.008	1.323	0.004	1.349	0.010	1.299	0.008	1.405	0.008	1.264	0.005	1.355	0.006	1.263	0.001	1.251	0.000	1.202	0.005	1.268	0.009	1.101	0.005	1.242	0.014	1.297	0.000	1.309	0.000	1.262	1.202	0.009	0.759	0.885	0.011	1.336	0.005	1.306	0.004	1.322	0.006	1.502	1.195	0.019	0.000	1.290	0.016	1.300	0.020	1.302	0.006	1.341	0.006	1.285	0.799	0.919	0.806	0.924	0.004	1.367	0.014	1.381	0.879	0.960	0.015	1.280	0.011	1.301	0.007	1.324	0.009	1.319	0.769	0.932	0.005	1.316	0.724	0.788	0.819	0.872	0.015	1.329	0.021	1.244	0.000	1.215	0.009	1.258	1.152	0.049	0.000	1.244	0.005	1.312	0.001	1.329	0.000	1.326	0.856	0.897	0.006	1.253	0.016	1.310	0.014	1.209	0.022	1.245	0.808	0.905	0.006	1.259	0.775	0.863	0.008	1.221	0.000	1.259	0.012	1.327	0.000	1.325	0.772	0.843	0.804	0.874	0.911	1.000	0.840	0.878	0.000	1.327	0.007	1.289	1.195	0.017	0.013	1.356	0.012	1.298	0.009	1.243	0.010	1.380	0.753	0.835	0.013	1.403	0.014	1.280	0.006	1.306	0.017	1.222	0.002	1.372
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