LOCO is implemented in GEMMA for the BIMBAM format. Pass in the -loco

1 switch for LOCO of chromosome 1.

What are the use cases?

1. User runs vanilla GEMMA: all SNPs are considered input for GWA and K
2. User passes in -snps: all these SNPs are considered for GWA and K
3. User passes in -snps and -ksnps: All these SNPs are used for GWA,
   Ksnps are used for K
4. User passes in -loco: SNPs are split by chromosome (GWA incl., K
   excl.)
5. User passes in -snps, -gwasnps and -ksnps could mean that also GWA
   is subset explicitely (nyi)

In all cases indicator_snp is honored and we get the most flexible way for
studying SNP combinations that can be passed in in different ways.

Overall added:

  - various comments in source code
  - tests in test framework inlc. fast-check
  - NDEBUG compilation support in the Makefile
  - -debug switch for GEMMA debug output
  - debug.h which includes enforce functions which work like
    assert. Unlike assert, enforce also works in release compilation
  - -nind switch limit the number of individuals used
    (trim_individuals for testing)
  - enforcing tests of input files - e.g. are number of individuals correct
  - checks for memory allocation - we should add more of those
  - more checks for gsl results - we should add more of those
  - replaced strtoken with regex as a first case. They should all be
    replaced. strtoken is not thread safe, for one.
  - introduced C++ iterators
  - introduced C++ closure in BimBam LMM for cached processing
  - more localized initialization of variables - makes for demonstratably
    more correct code
  - -ksnps adds snps into setKSnps
  - -gwasnps adds snps into setGWASnps
  - both sets are computed by -loco
  - attempted to make the code easier to read

2 files changed, 2000 insertions, 0 deletions

diff --git a/example/mouse_hs1940_snps.txt b/example/mouse_hs1940_snps.txt
new file mode 100644
index 0000000..9f20aa0
--- /dev/null
+++ b/example/mouse_hs1940_snps.txt
@@ -0,0 +1,1000 @@
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+rs3714431
+gnf02.119.284
+rs3680871
+rs4173052
+rs6299531
+rs13476463
+rs13478913
+rs6317860
+rs13478963
+rs3679473
+rs13476615
+rs3661039
+rs13480015
+rs6160140
+rs13483184
+rs13476330
+gnf14.019.954
+mCV23128319
+UT_3_89.066701
+rs13479879
diff --git a/example/mouse_hs1940_snps_anno.txt b/example/mouse_hs1940_snps_anno.txt
new file mode 100644
index 0000000..cfd4122
--- /dev/null
+++ b/example/mouse_hs1940_snps_anno.txt
@@ -0,0 +1,1000 @@
+rs3668922	111771071	13	65.0648
+rs13480515	17261714	10	4.72355
+rs13483034	53249416	17	30.175
+rs4184231	48293994	16	33.7747
+rs3687346	12815936	14	2.45302
+gnf10.000.619	NA	10	0.549798
+rs6258088	82616380	4	50.7375
+rs3657154	25351639	4	13.0781
+rs13459168	79615054	3	35.9488
+rs3699245	24926186	11	13.4081
+rs3692731	105981796	1	54.3948
+rs4184702	49429820	16	33.9562
+rs3716165	125938666	1	65.8444
+rs3692165	29620174	14	12.1522
+rs3690160	37015063	11	20.2587
+rs3696476	117118328	9	79.8486
+rs13478445	106983207	5	66.1267
+CEL-7_36442524	NA	7	26.3649
+mCV25307043	NA	5	84.4605
+rs8265673	102356580	11	70.912
+rs6395984	91070578	14	37.7522
+rs13476864	157465910	2	83.6744
+rs13466711	172135244	1	93.0543
+rs13478700	33297522	6	16.0349
+rs13481609	99263253	12	55.323
+rs3718784	25287148	11	13.5421
+rs4197715	67263247	16	44.0103
+rs3680765	49397123	7	26.522
+rs6355837	129713375	4	79.2943
+rs6245242	21478738	19	14.5837
+rs3703111	16785487	14	3.44733
+rs13482477	22519205	15	7.90254
+UT_4_58.126445	NA	4	42.0498
+rs13483569	23771627	19	18.6968
+rs3656008	43629190	17	20.1529
+rs3659698	11870131	11	5.15734
+rs3658914	130828039	3	64.9985
+rs3721822	131308159	6	75.661
+gnf06.123.229	NA	6	69.8894
+rs3684585	14560524	11	6.49166
+rs13483591	30814887	19	25.1448
+rs13479927	93955646	8	46.5649
+rs4158165	7646431	16	1.69797
+rs3685284	94188047	15	55.2232
+rs13476676	104099553	2	60.4366
+rs13478825	74688786	6	35.761
+rs6321462	43650849	4	27.5981
+rs13478553	138345042	5	91.1618
+CEL-9_99044286	NA	9	58.8985
+rs13478287	62118734	5	34.264
+rs3680026	113321137	7	60.9659
+rs13476066	114957525	1	56.8395
+rs3679483	180126256	2	107.324
+rs13479172	29340347	7	12.6872
+rs3698182	83587952	8	41.2234
+rs13481568	85150110	12	43.9983
+rs13478909	95383349	6	49.7836
+rs3154953	30187827	2	23.0095
+rs13481793	44884449	13	18.1255
+rs13481589	92176340	12	50.2606
+rs3694887	103735279	5	64.1859
+rs13481316	15555143	12	7.08188
+rs13479907	89381352	8	45.0234
+rs13476892	165396284	2	90.3273
+rs3700120	104500504	9	64.1947
+rs13477451	140714780	3	71.0701
+rs3701734	41327729	11	21.5451
+rs13482363	108252278	14	47.8535
+rs6272774	54180752	6	28.7966
+rs6292345	75301469	9	48.4366
+rs3710221	110389085	2	62.5863
+rs13481431	46801424	12	22.6927
+rs3653795	166630387	2	91.2977
+rs3702122	106416324	14	47.5675
+mCV23214561	NA	19	1.14225
+rs6204487	26131893	4	13.3102
+rs13477462	143558142	3	74.9115
+rs6211405	111717282	9	72.4166
+rs3089148	92941850	8	46.3161
+rs13478676	27655708	6	11.5581
+rs6296891	79983947	8	38.1803
+rs3705582	17603351	11	8.09978
+gnf03.160.792	NA	3	87.4855
+CEL-15_28995144	NA	15	10.5792
+mCV24786469	NA	1	112.529
+rs13482036	118384631	13	69.1715
+rs13477228	82436166	3	38.3819
+rs13475804	34929867	1	14.1453
+rs3706761	91989672	14	37.8867
+rs3663988	139319168	7	86.2784
+rs3676096	10671078	5	2.91098
+gnf11.093.105	NA	11	51.8811
+rs13479257	53778809	7	29.122
+rs13481511	68024081	12	31.0881
+rs6292169	56447533	8	28.4885
+rs13476966	8755001	3	0.445861
+rs13477985	131771792	4	80.6336
+rs13479540	133996942	7	81.1202
+petM-05233-3	NA	5	13.1446
+mCV23486224	NA	4	66.4078
+rs13480036	126607116	8	77.8966
+rs6328745	64264672	18	42.9404
+rs3699688	58957762	4	42.4062
+rs3695383	33796072	14	14.3559
+gnf17.082.284	NA	17	51.9272
+rs6184991	101697093	8	51.1608
+rs3714811	124207921	4	74.4119
+rs13476765	128474600	2	68.7832
+rs13475886	61171619	1	29.2939
+rs13459166	130541379	2	70.0231
+rs3701693	11135402	14	1.96294
+mCV24198179	NA	3	87.1922
+rs3670738	27325835	3	9.26999
+rs13479520	NA	7	73.2198
+rs4191367	59133145	16	38.4306
+rs13477553	9463709	4	3.01119
+mCV23994528	NA	1	109.078
+rs13483087	69269163	17	42.0473
+rs3673599	62806600	12	28.5686
+rs3674856	111217854	3	54.1693
+rs3711721	107226023	7	57.2408
+rs6241342	119182633	7	64.4351
+rs6223687	81780432	9	51.8775
+rs3703161	128357744	8	79.7733
+rs3684732	83007814	17	53.9756
+rs13482419	4301393	15	0.1
+rs6354478	6241050	5	2.26507
+rs13483066	63320298	17	35.254
+rs13477048	33086267	3	15.767
+rs13480180	48420735	9	30.3166
+rs6226936	158845979	1	80.054
+rs13482579	52834896	15	21.0118
+rs13481764	36557616	13	11.5364
+rs3674369	23210432	15	8.30254
+rs13480758	108473286	10	62.7941
+rs6340166	72797040	5	41.6748
+rs3723670	52514798	9	32.2421
+gnf17.042.585	NA	17	19.521
+rs6313528	19045014	11	8.81978
+rs13477335	116920487	3	56.0978
+CEL-7_116160192	NA	7	73.3692
+rs4172338	34723432	16	26.7945
+rs6157345	95619583	1	52.9014
+rs13476963	7679816	3	0.192857
+rs3722255	63336847	3	29.8132
+rs3696823	19105543	15	7.47134
+rs3689263	74311123	2	46.3781
+rs3090818	13826959	14	2.55302
+rs3663068	18736595	14	5.03702
+rs3713432	78097862	7	41.4979
+rs13481961	97270237	13	51.6175
+rs13479091	147487801	6	89.333
+rs13481583	90350885	12	48.6582
+gnf08.055.205	NA	8	28.4778
+rs13478679	28352522	6	11.6127
+rs6409039	94162742	12	50.9036
+rs13476714	115139005	2	64.0296
+rs3654545	72091954	17	44.1973
+rs3703836	100585663	15	63.0016
+rs13481588	91968729	12	50.1599
+rs6185483	55235582	19	50.2192
+rs3663873	110177041	3	53.8391
+rs3023339	24804820	12	8.97317
+rs6190892	10474677	15	4.23068
+rs3706317	61091492	3	29.2317
+CEL-3_59059215	NA	3	28.6449
+rs3664897	67499597	13	32.9733
+rs13478971	111299794	6	59.1094
+rs3691210	157995224	2	83.8744
+rs6315432	46233922	5	27.8612
+rs13479676	30360115	8	16.2089
+rs3721068	113915010	9	75.0971
+rs13482474	22155623	15	7.61826
+rs4223211	69796844	2	42.153
+rs3023058	135829456	5	88.8705
+rs13482928	25964330	17	10.451
+rs13483639	44191430	19	38.0252
+rs4139897	47856079	18	26.9405
+rs3726927	141075115	1	72.6875
+rs3713702	64271271	11	36.9088
+rs13459134	115271947	11	88.401
+rs13481751	33720509	13	10.223
+rs13481640	108205932	12	64.8493
+rs13481804	47603346	13	20.193
+rs3714819	55350965	17	31.1628
+CEL-5_45716874	NA	5	28.0401
+UT_5_103.462256	NA	5	64.5011
+rs6153168	8299968	8	1.10444
+rs13479887	88295611	8	44.4278
+rs4140148	150476349	4	95.9108
+rs6159786	29684270	14	12.2408
+rs13480315	84973533	9	52.9101
+rs13480653	74981224	10	43.0295
+rs3694708	160008042	2	85.8928
+rs13478048	150309421	4	95.8765
+rs3692387	126903210	5	80.2873
+rs3703247	45999569	7	24.6749
+rs13477401	129579191	3	62.7618
+rs4228112	13009201	10	2.58728
+rs13475757	21286957	1	5.9138
+rs3721056	71032448	9	44.4738
+rs4222732	156808590	1	79.3212
+UT_6_136.421356	NA	6	77.9665
+rs13477902	108638296	4	66.3258
+rs13461280	111266995	12	66.858
+rs3676884	94921847	4	58.1594
+rs3721457	117687044	7	64.2093
+rs3722149	34756708	7	17.1813
+rs3657482	114065685	7	61.3477
+rs13476475	46764454	2	29.2929
+rs3695693	9619040	9	0.086045
+rs3700085	119673759	9	82.4914
+rs13476804	139496332	2	76.2408
+rs3706023	73054685	17	45.1552
+rs13479825	83183210	8	40.8723
+rs6317800	96894089	2	57.0795
+gnf17.083.842	NA	17	53.508
+rs13483606	36056602	19	30.2593
+rs6380191	39627107	3	20.1768
+rs13478677	27951181	6	11.5812
+rs6301349	96146686	14	39.3196
+rs3710581	36397464	19	31.8693
+rs4174474	38174823	16	29.3054
+gnf05.084.686	NA	5	53.0968
+rs6314716	40617203	14	15.8064
+rs4137234	67539780	13	32.9929
+UT_8_130.396331	NA	8	80.4067
+rs13475883	59379132	1	28.543
+mCV23508321	NA	11	13.8615
+rs13481021	51107253	11	27.7449
+rs4222215	23996126	1	9.03999
+CEL-15_15740145	NA	15	6.89363
+rs3674193	178717320	2	104.867
+rs6328956	63898025	4	43.9073
+gnf05.124.749	NA	5	84.3148
+UT_11_75.985289	NA	11	45.4302
+rs6276149	98443248	7	54.5189
+rs6299927	92435165	14	37.9519
+mCV24107897	NA	1	4.04864
+rs13475722	10754229	1	2.6061
+rs3674066	149681877	3	80.9788
+rs3695308	33703006	3	16.0978
+rs13483207	11226999	18	4.2883
+rs3686912	64326546	11	36.9343
+rs13478738	46837420	6	24.0994
+rs8257588	47863308	19	40.8718
+rs13480275	73613909	9	45.4436
+rs3705458	99300806	5	61.4322
+rs13476378	22396323	2	14.8814
+rs13475963	NA	1	48.7321
+rs13478983	114263350	6	61.2351
+rs13481480	59142685	12	27.809
+rs6209043	89939632	4	54.6618
+rs13477130	57833682	3	27.879
+rs6409040	49076611	15	18.363
+rs13483178	94236078	17	63.0775
+rs4224501	56744581	4	39.532
+rs13480194	52312797	9	32.1413
+rs3714056	68879859	13	33.6366
+rs3705396	85421292	3	39.7315
+rs13477083	43525954	3	21.2979
+rs4139262	8919487	19	1.97111
+mCV23822994	NA	17	8.73244
+rs13475774	26044918	1	9.60917
+rs13482109	27631766	14	11.2008
+CEL-7_41997914	NA	7	29.2827
+CEL-10_74277238	NA	10	42.8842
+rs3022934	133563227	2	73.1717
+CEL-6_84629314	NA	6	40.551
+rs4228452	111294252	10	64.1812
+rs13480988	41682478	11	21.6189
+UT_8_72.075442	NA	8	32.7213
+rs6201966	19844417	7	2.78979
+rs8244157	54618045	14	18.5842
+rs3663375	93316837	10	54.9628
+rs6353774	59723178	1	29.093
+rs6185261	12011734	11	5.28424
+rs3713696	23486604	9	7.56987
+gnf02.026.314	NA	2	22.6103
+rs6343757	6027976	6	1.47261
+rs13477378	122515116	3	59.6775
+rs3715857	19251978	15	7.47391
+rs13478798	64385626	6	32.4757
+CEL-5_56325748	NA	5	33.8212
+rs13480659	77467415	10	45.1763
+rs13478839	77811523	6	39.1209
+rs6187389	86170027	15	43.1673
+rs4136879	41440054	2	26.8189
+rs6281838	129945301	1	67.5078
+rs13476304	191230917	1	114.102
+gnf14.103.048	NA	14	47.6719
+UT_3_105.614392	NA	3	49.9643
+rs13480601	44306419	10	21.5679
+rs13483549	18156623	19	11.4771
+rs6223790	25520164	5	14.5473
+rs6298808	49216689	10	24.4764
+rs6263067	127168237	1	66.4928
+rs3669513	15559838	1	4.49129
+rs6260116	65803230	7	31.4936
+rs3664869	96886065	8	49.3778
+rs13482084	12241471	14	1.97196
+gnf10.082.230	NA	10	46.6722
+rs13483020	50512518	17	28.41
+rs3660486	32027092	17	14.5449
+rs3721276	14365170	3	1.72857
+CEL-5_117374791	NA	5	75.939
+rs3708633	118743250	13	69.5115
+gnf01.059.986	NA	1	29.9036
+rs13483358	50687407	18	28.7903
+mCV25009162	NA	5	100.287
+rs3694629	7565278	17	3.30346
+rs6186560	36105285	9	21.6087
+rs3710202	33692194	6	16.198
+rs13479768	54356344	8	28.4475
+rs13481308	13326947	12	5.82788
+rs3672124	110615073	12	66.5493
+rs13482714	92843376	15	53.8644
+rs3683699	30504073	18	16.2736
+rs4226572	44304449	7	23.8749
+rs13479694	34211730	8	19.8181
+rs6224522	90610312	3	41.1674
+rs13481041	56701595	11	30.6467
+rs3674364	84313424	13	44.1566
+rs13477030	27601284	3	9.34774
+rs13480845	5635235	11	1.91167
+rs8246989	7614643	3	0.121366
+rs6380710	26214430	1	10.0092
+UT_9_82.824657	NA	9	51.354
+rs6238322	28056254	19	22.4092
+rs6353097	14805061	5	5.75677
+gnf01.126.387	NA	1	66.0094
+rs4174329	38079234	16	29.2566
+rs3695075	101550815	12	56.7889
+rs6262666	41652135	1	20.5225
+rs13476186	153891983	1	76.4535
+mCV24130963	NA	19	0
+rs4139548	20371773	2	14.1165
+rs4226870	118119561	7	64.3133
+rs13476750	123655476	2	66.8472
+mCV22528760	NA	2	64.9448
+rs3702484	9688352	17	5.26721
+rs8252588	3713237	7	0.0234926
+rs13477692	48886872	4	31.7633
+UT_2_129.88318	NA	2	69.9554
+rs13482668	80923574	15	40.2533
+rs13459184	95122411	3	44.0512
+rs3700313	17681589	11	8.16015
+rs6371982	34135438	3	16.9723
+rs3700592	92343344	13	48.1792
+rs4211364	80830072	16	52.1212
+rs6229068	106516721	7	57.1148
+rs3667772	60168778	3	29.0757
+rs13480991	42821191	11	22.2087
+rs13482482	24593717	15	8.51311
+rs3689073	7385255	3	0.0958321
+rs13482731	97760644	15	59.8722
+rs3698196	86127915	3	39.7781
+mCV23893269	NA	9	0
+rs13482306	91549652	14	37.8223
+gnf10.004.839	NA	10	0.949684
+rs6241299	85595434	4	51.744
+rs13483217	14112799	18	5.68026
+mCV24217147	NA	10	71.1244
+rs3723643	122318583	2	66.64
+rs13483476	84649628	18	62.872
+rs6328018	26133356	12	10.1958
+rs13477019	23824920	3	7.72032
+rs3688968	119721407	4	71.3737
+CEL-14_90299389	NA	14	40.2483
+rs3676394	85374875	18	63.0525
+rs4222922	193272691	1	117.136
+rs13476081	119860126	1	58.2392
+rs13481650	111188138	12	66.8118
+rs13479188	35339838	7	17.7493
+rs3707749	63100183	17	35.1897
+rs3655334	118448960	7	64.3432
+rs3676100	13307520	14	2.50164
+rs13477594	20288095	4	9.69074
+rs3680100	21919402	18	10.2863
+rs3726406	112713037	4	67.3946
+rs3663355	48113334	4	31.5662
+rs13483149	86990367	17	59.774
+rs3668028	86433604	14	36.6159
+rs13477790	77633242	4	47.989
+rs13478413	99002935	5	61.4213
+rs13479197	37796997	7	21.0346
+petM-02162-1	NA	19	12.7818
+mCV24423497	NA	13	45.1619
+rs3705394	13565037	11	6.1493
+CEL-15_9687257	NA	15	2.71222
+rs3679120	22921279	10	8.01228
+rs6241653	133096673	1	68.2746
+rs13477092	47207215	3	21.6659
+mCV24338392	NA	17	8.98278
+CEL-7_64160024	NA	7	41.3808
+rs3709567	126209771	8	75.9823
+rs13476067	115261364	1	56.9937
+rs3670749	52959274	12	24.1983
+rs6361711	42638721	5	25.4031
+UT_13_4.391534	NA	13	0.0406796
+rs6245643	92582795	4	56.7146
+rs6212085	15901251	5	6.29309
+rs3706792	78990729	14	34.3249
+rs3703728	51409446	7	28.0787
+rs4185336	50013921	16	34.4523
+rs13477717	55490244	4	35.9432
+rs3718386	120762044	2	66.4325
+mhcCD8a2	NA	6	34.5609
+rs3676101	26196372	5	15.2652
+rs13480536	21933905	10	7.18871
+rs8253516	68882191	8	32.1055
+rs3689218	19023811	7	1.89155
+rs13476950	3785419	3	0.00564417
+rs3698001	100446376	12	56.4327
+rs13481791	44207516	13	18.0616
+rs3691938	68266513	5	40.0212
+rs3685822	64093541	9	38.7064
+rs3658897	32553900	12	13.9304
+rs3687275	43070188	19	36.8259
+UT_15_87.526763	NA	15	42.9087
+mCV23209429	NA	2	23.8655
+rs6230167	52546441	1	25.9716
+rs8236770	83672212	8	41.2256
+rs3694989	66158607	9	39.979
+rs13480358	96686737	9	57.9811
+rs13476077	118975178	1	57.8821
+rs3023025	143182416	4	90.5694
+rs13477904	109080466	4	66.4292
+CEL-7_43463457	NA	7	29.4967
+rs13477072	40459556	3	20.5114
+rs13478750	50520106	6	26.5327
+UT_17_25.804649	NA	17	10.4846
+rs6209951	94400523	11	57.079
+rs6162256	80059839	4	48.9979
+rs6305232	153227479	1	76.153
+rs13480400	106647931	9	66.2224
+rs3681670	52031205	14	18.5124
+rs3675388	152670038	2	81.6619
+rs4219590	92046041	16	59.4329
+rs3671174	28101343	18	15.114
+rs6239372	34698851	7	17.1564
+rs4197422	50582943	14	18.4722
+rs13475872	53011522	1	26.0101
+rs6261913	138649668	6	80.9736
+CEL-15_74419628	NA	15	35.7485
+rs6413270	37941444	9	22.0292
+rs3683507	79200892	3	35.9255
+rs3673976	43329014	19	36.8352
+rs6403494	54826720	17	30.9164
+rs13477493	151419353	3	81.4861
+rs6408534	35432115	5	20.2374
+mCV23717969	NA	4	8.05003
+CEL-6_8231384	NA	6	2.66868
+CEL-4_74066970	NA	4	47.4533
+rs3677115	40583019	19	34.61
+rs3696518	43956027	6	23.0561
+rs13478995	117470880	6	63.9779
+rs13477188	72112256	3	33.1754
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+rs3682333	31949698	5	19.2374
+rs3714102	101893149	5	61.9542
+rs6220667	174204401	1	95.3999
+rs3711084	102307079	13	54.7342
+rs3023233	28596047	10	14.5969
+rs3726250	53008551	4	34.4287
+rs3705677	40419685	5	23.85
+rs6303064	19600292	18	8.2778
+rs13479287	62079258	7	30.5235
+CEL-1_140926026	NA	1	72.6592
+rs4165029	16262762	16	10.7089
+rs6353593	68424814	2	41.0552
+rs13475789	30005368	1	10.6518
+rs3684964	64661178	18	42.9849
+rs3021887	118115231	2	65.6914
+rs4227074	23448883	8	10.0443
+rs3688343	34272795	12	15.285
+CEL-19_34542259	NA	19	30.0494
+CEL-4_118427459	NA	4	72.0372
+rs13480907	22220570	11	11.8791
+rs3682128	37262913	14	15.2686
+rs3654569	52550668	9	32.2468
+rs3708061	81304223	4	49.1775
+rs13480114	26961500	9	10.8423
+rs13482620	66244636	15	32.0154
+rs3702451	102120297	13	54.6506
+rs8254782	115490033	6	61.9184
+rs4229363	53150467	12	24.2016
+rs3702220	80737850	13	40.6781
+rs3662056	105105757	4	64.7232
+rs3661718	144810830	2	77.9934
+gnf10.122.050	NA	10	75.6302
+CEL-17_91044280	NA	17	62.9279
+rs13477457	142436681	3	73.841
+rs13482013	111021030	13	64.6391
+rs13480721	97521558	10	57.1833
+rs13483472	83748624	18	62.6477
+rs3677807	106694559	8	55.5849
+rs3688854	20281706	2	14.0579
+gnf13.008.720	NA	13	1.56575
+rs13478015	139155261	4	86.1166
+rs6281562	126292376	1	65.9182
+rs13482331	98520204	14	40.473
+rs3700038	40378101	13	15.8963
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+rs3672425	68346128	14	27.0922
+rs3662930	115522043	11	88.4566
+CEL-12_87311152	NA	12	50.508
+rs3662436	68825035	13	33.6148
+rs3708442	192343890	1	116.059
+rs3673457	81859840	9	51.9022
+rs6225875	117143301	14	52.1314
+rs3709561	44222161	15	16.1091
+mCV22965443	NA	17	16.8477
+gnf05.136.579	NA	5	96.0368
+rs3694949	38455561	9	22.1334
+mCV23446189	NA	3	62.2481
+rs13480443	117512156	9	80.2729
+rs3685643	162250061	1	81.8151
+rs6379062	54154770	9	32.9995
+rs13476062	114013439	1	56.3604
+UT_15_101.086192	NA	15	60.6777
+rs13459146	34517940	15	13.1797
+rs13477775	73942635	4	46.1614
+rs6255802	50772424	12	23.5146
+gnf10.130.258	NA	10	82.4073
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+rs3721803	7003954	10	0.0282926
+rs4227587	32754921	9	16.4785
+rs3676483	44938143	18	25.1621
+mCV22625013	NA	11	87.2647
+rs13482065	14353510	14	2.75302
+rs3698600	15055680	14	2.83797
+rs13481410	40842857	12	20.3982
+rs3727022	104351877	2	60.6366
+gnf08.031.589	NA	8	18.1181
+rs6263485	90009339	2	53.1725
+rs6188665	65422955	16	41.0204
+rs13483016	49557882	17	27.621
+rs3722112	119168908	7	64.4331
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+rs6217010	96031708	3	44.6523
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+rs3667748	16644045	17	7.23965
+rs13480251	66990365	9	40.4916
+UT_6_5.754097	NA	6	1.47255
+rs6196597	104974507	10	61.2507
+rs3678364	11077682	10	1.77062
+rs6342608	78159752	15	38.865
+rs3695107	70414591	5	40.4936
+rs6370750	49485509	5	29.1957
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+rs3654251	23990827	5	10.7105
+rs3672987	33110220	17	16.0344
+gnf13.057.762	NA	13	28.499
+rs13481985	98646123	13	52.1827
+rs3655885	45438349	1	23.3298
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+rs3665127	39413046	1	18.0974
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+rs3695382	36324656	12	17.4139
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+rs13483212	12110690	18	4.51687
+rs13478952	106305503	6	56.6647
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+rs3656875	68196791	8	31.9452
+rs3697020	125538952	2	67.8524
+rs4172185	34466988	16	26.725
+mCV22595554	NA	9	39.7043
+rs13481855	65296578	13	32.5145
+UT_17_75.437568	NA	17	47.0353
+rs3660588	30328765	3	13.2523
+rs3687764	95749389	4	58.6842
+rs6366840	29150899	19	23.2882
+rs3023981	70099153	4	45.8222
+mCV24436061	NA	8	23.0116
+rs13481070	65095597	11	37.9938
+rs3655057	13383077	12	5.85244
+gnf03.067.696	NA	3	33.0652
+rs6185468	70243524	14	27.7446
+rs13479880	86747129	8	42.9433
+rs4197693	67131002	16	43.9926
+mCV23045722	NA	19	39.618
+gnf07.129.013	NA	7	79.2206
+rs6170261	59044168	16	38.3828
+gnf10.009.098	NA	10	1.86089
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+rs3684103	94242458	4	57.7461
+rs3688141	75192214	17	47.297
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+rs3670168	128292534	3	61.6118
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+rs13479329	72269923	7	38.9093
+rs13481462	54640358	12	25.3172
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+rs3712524	169850145	1	89.6632
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+rs6390142	78868207	13	40.2396
+rs3724616	3000665	17	0
+rs4227609	44391960	9	28.3837
+mCV23575714	NA	1	115.926
+rs6364065	23474991	7	2.88943
+rs8275764	65231542	4	44.0691
+rs13480454	120697838	9	82.8681
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+rs4223701	181516393	2	108.339
+rs13478053	151285670	4	96.9651
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+mCV23851630	NA	11	6.02756
+rs4219905	92999666	16	60.0987
+gnf12.013.284	NA	12	7.33577
+rs13478398	93725627	5	60.0184
+gnf14.013.298	NA	14	5.98588
+rs6374597	110506551	9	70.1087
+rs3023265	57760615	11	32.0606
+rs13475785	28820258	1	10.369
+mCV24528954	NA	3	29.874
+rs6187777	141124127	2	76.8726
+rs6208887	86407128	17	59.5461
+gnf08.098.331	NA	8	49.439
+rs4232105	23165771	19	17.9673
+rs3655098	68648726	9	42.2188
+gnf03.079.138	NA	3	37.9533
+rs6272967	39325001	8	22.1753
+CEL-8_7689226	NA	8	0.934165
+rs3671527	99145299	4	60.3594
+rs6335368	9779999	11	4.00031
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+rs3686804	79333348	3	35.933
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+rs13481456	52868858	12	24.1968
+rs13477807	83002718	4	50.844
+CEL-1_101048458	NA	1	54.0781
+rs3666667	30760759	15	11.2639
+rs13475964	86305558	1	48.7524
+rs3704471	126179960	2	67.88
+rs13459095	149946882	5	106.163
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+rs13480023	122762890	8	72.8859
+rs13477952	122951885	4	74.1086
+rs3718641	53706897	7	29.0918
+mCV22331476	NA	18	30.7475
+rs13481702	14756099	13	2.29972
+UT_4_57.645957	NA	4	41.0374
+rs3659348	104390684	7	56.2984
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+rs3663650	41882900	8	22.7548
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+mCV24380249	NA	1	51.0885
+rs3723136	92666016	6	44.8436
+rs6238153	95354108	11	57.2209
+rs13482509	32042169	15	12.0618
+gnf18.014.547	NA	18	7.83115
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+rs3679439	97128561	8	49.4815
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+CEL-9_17007263	NA	9	3.44286
+rs6358447	97626757	1	53.3083
+rs13477303	103988744	3	50.1972
+UT_11_29.443258	NA	11	14.9225
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+rs3682341	68078502	17	40.7239
+gnf19.005.316	NA	19	1.23778
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+UT_2_70.039995	NA	2	42.1196
+rs4223511	131993535	2	71.8356
+rs3088491	12430080	15	4.73955
+rs13483438	74218827	18	54.9736
+CEL-3_137067761	NA	3	67.9901
+rs3675505	95138968	1	52.8545
+CEL-4_6055375	NA	4	0.85
+rs3656005	45334674	19	39.0591
+CEL-8_94486767	NA	8	47.6569
+rs4152838	5029450	16	0.060615
+rs6244900	82656865	17	53.654
+rs3660226	66950667	12	30.0297
+rs4231834	44021991	18	24.869
+CEL-9_98918429	NA	9	58.8341
+UT_3_89.90208	NA	3	40.7882
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+rs13480856	7952877	11	2.875
+rs13478502	124000381	5	78.3279
+gnf09.028.495	NA	9	17.9921
+mCV24205612	NA	10	61.6863
+CEL-4_78089985	NA	4	48.9627
+rs4165510	27359166	16	19.5495
+rs3680197	44208892	2	28.02
+rs4223969	55049341	3	26.23
+rs13479476	116888764	7	63.592
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+CEL-7_122606289	NA	7	83.7589
+gnf02.161.674	NA	2	84.0244
+rs8255228	125914815	3	60.8674
+rs13478733	45626021	6	23.6075
+UT_14_10.122547	NA	14	2.80698
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+rs3709732	117966892	3	57.3639
+rs3682937	4680332	11	0.368248
+rs13477065	38106857	3	19.7519
+CEL-13_22517579	NA	13	5.97895
+rs13475064	88909952	3	41.0153
+rs4226048	83769061	6	40.4709
+gnf11.098.224	NA	11	55.8043
+rs13481380	32097332	12	13.8492
+CEL-5_15079682	NA	5	7.01831
+rs4219072	91372335	16	58.9792
+rs13481012	47164882	11	25.2198
+rs3702472	68091016	8	31.8841
+rs13478051	150948093	4	96.0396
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+gnf19.052.359	NA	19	47.1283
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+rs3724411	30763164	12	13.2573
+rs3708313	100432682	7	55.1222
+rs13480065	9290508	9	0.0798989
+rs6265656	156863894	2	83.2744
+CEL-2_168918742	NA	2	92.6145
+rs3718133	48701997	18	27.1292
+rs13481827	57777869	13	27.279
+rs3703241	57632187	17	32.2351
+rs3162895	64201441	1	31.943
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+rs13480451	119956886	9	82.5477
+rs13479823	71315172	8	32.558
+gnf10.055.290	NA	10	28.0444
+rs3726588	82107859	13	42.8688
+mCV22794972	NA	9	50.157
+rs4221957	129825026	3	63.6595
+rs3695907	10708690	11	4.22495
+rs6357455	138894858	3	69.0818
+rs3719497	25502498	17	10.2689
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+rs13479419	96873989	7	53.5015
+rs13478796	63559836	6	32.2792
+rs3658433	84048258	11	51.3069
+rs13480436	114920618	9	77.1771
+rs3717846	64516102	7	30.9685
+gnf12.060.469	NA	12	28.5514
+rs3692487	5455372	2	1.63333
+UT_4_32.135337	NA	4	15.6675
+rs13478522	128472892	5	82.0077
+rs3683834	58573929	17	32.6778
+rs3667738	38492075	8	22.0235
+rs13459110	71483232	9	44.5914
+CEL-3_156007479	NA	3	85.6353
+rs3655717	65465164	9	39.5517
+rs13476607	82857454	2	52.0807
+rs13479239	50250025	7	27.4887
+mCV23970227	NA	1	117.959
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+rs13483579	27168119	19	21.6241
+rs13479763	53255231	8	28.4346
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+gnf14.018.589	NA	14	9.63075
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+mCV25230888	NA	8	8.22771
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+gnf09.020.405	NA	9	9.92649
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+rs4136200	76792153	6	36.8737
+gnf07.061.149	NA	7	32.2117
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+rs3698831	22282024	15	7.73826
+rs6307147	149955081	3	81.0356
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+UT_2_144.017259	NA	2	77.8769
+rs13478215	43916770	5	25.9162
+rs6343029	102342395	8	51.1738
+rs13478370	85461198	5	52.1106
+CEL-12_87170441	NA	12	50.4505
+rs6362861	29524193	17	12.9715
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+CEL-11_121219118	NA	11	93.4868
+rs6315002	103049359	4	62.6978
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+rs13476368	19754856	2	13.199
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+rs13476530	60018236	2	35.735
+CEL-3_94149786	NA	3	43.4168
+rs13475888	61832866	1	29.7573
+UT_17_86.377392	NA	17	57.3467
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+gnf09.016.676	NA	9	6.9609
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