Added F3-outbred example.

examples/F3-outbred/F3-outbred_A.gen

+data type A
+1 37 0 0
+*M_1_1 2
+*M_1_2 2
+*M_1_3 2
+*M_1_4 0
+*M_1_5 2
+*M_1_6 2
+*M_1_7 2
+*M_1_8 2
+*M_1_9 0
+*M_1_10 2
+*M_1_11 2
+*M_1_12 2
+*M_1_13 2
+*M_1_14 2
+*M_1_15 0
+*M_1_16 0
+*M_1_17 0
+*M_1_18 0
+*M_1_19 2
+*M_1_20 0
+*M_2_1 0
+*M_2_2 0
+*M_2_3 2
+*M_2_4 0
+*M_2_5 0
+*M_2_6 0
+*M_2_7 0
+*M_2_8 0
+*M_2_9 2
+*M_2_10 2
+*M_2_11 0
+*M_2_12 0
+*M_2_13 2
+*M_2_14 0
+*M_2_15 0
+*M_2_16 0
+*M_2_17 0

examples/F3-outbred/F3-outbred_B.gen

+data type B
+1 37 0 0
+*M_1_1 2
+*M_1_2 2
+*M_1_3 2
+*M_1_4 0
+*M_1_5 2
+*M_1_6 0
+*M_1_7 0
+*M_1_8 2
+*M_1_9 0
+*M_1_10 0
+*M_1_11 0
+*M_1_12 2
+*M_1_13 0
+*M_1_14 0
+*M_1_15 2
+*M_1_16 0
+*M_1_17 2
+*M_1_18 0
+*M_1_19 0
+*M_1_20 0
+*M_2_1 2
+*M_2_2 2
+*M_2_3 2
+*M_2_4 0
+*M_2_5 0
+*M_2_6 0
+*M_2_7 0
+*M_2_8 2
+*M_2_9 2
+*M_2_10 2
+*M_2_11 0
+*M_2_12 0
+*M_2_13 2
+*M_2_14 0
+*M_2_15 0
+*M_2_16 2
+*M_2_17 2

examples/F3-outbred/F3-outbred_C.gen

+data type C
+1 37 0 0
+*M_1_1 0
+*M_1_2 0
+*M_1_3 2
+*M_1_4 2
+*M_1_5 2
+*M_1_6 2
+*M_1_7 0
+*M_1_8 2
+*M_1_9 2
+*M_1_10 0
+*M_1_11 2
+*M_1_12 2
+*M_1_13 2
+*M_1_14 2
+*M_1_15 2
+*M_1_16 0
+*M_1_17 0
+*M_1_18 2
+*M_1_19 2
+*M_1_20 2
+*M_2_1 0
+*M_2_2 2
+*M_2_3 2
+*M_2_4 0
+*M_2_5 0
+*M_2_6 2
+*M_2_7 0
+*M_2_8 2
+*M_2_9 2
+*M_2_10 2
+*M_2_11 2
+*M_2_12 2
+*M_2_13 -
+*M_2_14 2
+*M_2_15 2
+*M_2_16 0
+*M_2_17 0

examples/F3-outbred/F3-outbred_D.gen

+data type D
+1 37 0 0
+*M_1_1 2
+*M_1_2 0
+*M_1_3 2
+*M_1_4 0
+*M_1_5 -
+*M_1_6 2
+*M_1_7 2
+*M_1_8 2
+*M_1_9 -
+*M_1_10 0
+*M_1_11 2
+*M_1_12 2
+*M_1_13 0
+*M_1_14 0
+*M_1_15 0
+*M_1_16 0
+*M_1_17 2
+*M_1_18 2
+*M_1_19 0
+*M_1_20 0
+*M_2_1 0
+*M_2_2 0
+*M_2_3 0
+*M_2_4 2
+*M_2_5 2
+*M_2_6 2
+*M_2_7 0
+*M_2_8 2
+*M_2_9 2
+*M_2_10 0
+*M_2_11 0
+*M_2_12 0
+*M_2_13 0
+*M_2_14 0
+*M_2_15 0
+*M_2_16 0
+*M_2_17 0

examples/F3-outbred/README

+This dataset is a simulated population with the following structure :
+
+ A(1) B(1)  C(1)   D(1)
+   \  /       \   /
+   AB(100)   CD(100)
+      \      /
+       F1(100)
+          |
+       F2(100)
+          |
+       F3(1000)
+
+It features SNP-like observations encoded as 0, 1, and 2, on all four ancestors and the F3 individuals. About 2% of the data is missing.
+The genetic map features two chromosomes respectively 150cM and 120cM long with respectively 20 and 17 markers.
+
+Three traits (t1, t2, t3) are simulated for F3:
+- t1 on QTL M_2_14 on chromosome ch2 at 104.61cM, with effects A=20, B=30, C=10, D=0, and a small gaussian noise.
+- t2 on QTL M_2_14 on chromosome ch2 at 104.61cM, with effects A=100, B=10, C=0, D=200, and a small gaussian noise.
+- t3 on QTL M_2_9 on chromosome ch2 at 52.56cM, with effects A=5, B=3, C=6, D=4, and a small gaussian noise.
+
+The commands to run spell-qtl are :
+
+$ spell-pedigree -wd spell -n demo -p F3-outbred.ped
+
+$ spell-marker -n demo -wd spell -m A:02 F3-outbred_A.gen -m B:02 F3-outbred_B.gen -m C:02 F3-outbred_C.gen -m D:02 F3-outbred_D.gen -m F3:02 F3-outbred_F3.gen -o F3
+
+$ spell-qtl -n demo -wd spell/ -gm F3-outbred.map -p F3 F3-outbred_F3.phen -P auto QTL-detection CIM-
+
+
+To output the 1-point Parental Origin Probabilities, add -O1 to the spell-marker commandline.
+To output the n-point Parental Origin Probabilities, add output-nppop to the spell-qtl commandline.
+To run spell-marker multi-threaded, add -mt <number of cores> to the spell-marker commandline.

examples/three_parents_F2/README

+This dataset is a simulated population with the following structure :
+
+A(1) B(1)    C(1)
+ \  /   \   /
+  F1(1)  F1C(1)
+  |        |
+ F2(100)  F2C(100)
+
+The genetic map features two chromosomes respectively 150cM and 120cM long with respectively 20 and 17 markers.
+
+One trait (t1) is simulated for F2 and F2C, affected by two QTLs:
+- one on chromosome 1 on marker M_1_4 at 14.97cM, with effects A=1, B=0, C=-1, and gaussian noise with parameters (mu=0, sigma=2)
+- one on chromosome 2 on marker M_2_6 at 68.37cM, with effects A=1, B=0, C=-1, and gaussian noise with parameters (mu=0, sigma=1)
+
+
+The commands to run spell-qtl are :
+
+$ spell-pedigree -wd spell/ -n demo -p example1.ped
+
+$ spell-marker -n demo -wd spell -m F2:A/B example1_F2.gen -m F2C:A/C example1_F2C.gen -o F2,F2C
+
+$ spell-qtl -n toto -wd spell -p F2 example1_F2.phen -p F2C example1_F2C.phen -gm example1.map -P auto QTL-detection CIM connected
+
+The connected parameter forces spell-qtl to consider A as the same ancestor in F2 and F2C. You can remove this parameter and see the difference in the final model.
+To output the 1-point Parental Origin Probabilities, add -O1 to the spell-marker commandline.
+To output the n-point Parental Origin Probabilities, add output-nppop to the spell-qtl commandline.
+To run spell-marker multi-threaded, add -mt <number of cores> to the spell-marker commandline.