About ready to tag for alpha release.

CMakeLists.txt

@@ -117,6 +117,7 @@ endfunction()
 add_manpage(spell-pedigree.1)
 add_manpage(spell-marker.1)
 add_manpage(spell-qtl.1)
+add_manpage(spell-qtl-examples.1)
 
 #add_custom_command(OUTPUT spell-marker.1
 #        COMMAND pandoc -t man ${CMAKE_SOURCE_DIR}/doc/man/spell-marker.1.md -o spell-marker.1

doc/man/spell-marker.1.md

@@ -8,7 +8,7 @@ spell-marker – Compute the 1-point Parental Origin Probabilities in a pedigree
 
 # SYNOPSIS
 
-**spell-marker** [options...] **-n** *NAME* **-p** *FILE* **-m** *GEN:FORMAT* *FILE* [**-m**...]
+**spell-marker** [options...] [**--wd** *PATH*] **-n** *NAME* **-m** *GEN:FORMAT* *FILE* [**-m**...]
 
 # DESCRIPTION
 
@@ -20,11 +20,13 @@ perform the actual QTL analysis.
 Because each marker is supposed to be independent, **spell-marker** can perform the computations in parallel in a
 variety of ways. See the *Job control* subsection of the options for details.
 
-**-n**,**--name** *population_name*
-: The name of this population (will also be used to create the output filename)
+**spell-marker** expects that **spell-pedigree** has been run  beforehand with the same working directory and configuration name.
 
-**-p**,**--pedigree** *FILE*
-: Path to the output from spell-pedigree.
+**-wd**,**--work-directory** *PATH*
+: Path to directory for cache files and outputs. Defaults to the **current directory**.
+
+**-n**,**--name** *NAME*
+: User-friendly name for this configuration
 
 **-m**,**--marker-obs** *GEN:FORMAT* *FILE*
 : Path to the marker observations file of generation *GEN* with given format *FORMAT*. This file must have as many
@@ -54,9 +56,6 @@ individuals as the pedigree has for that generation.
 **-z**,**--noise** *level*
 : Set the noise level for marker observations. Defaults to **0**.
 
-**-wd**,**--work-directory** *path*
-: Path to directory for output files. Defaults to the **current directory**.
-
 ## Job control
 
 Select and configure the job control scheme
@@ -92,11 +91,13 @@ Set the output mode. By default, only the population data file will be written.
 Parental Origin Probabilities will be written, unless you also specify -Op.
 
 **-Op**,**--output-population-data**
-: Output the population data file for use in spell-qtl. This is the default behaviour.
+: Output the population data file for use in spell-qtl. This is the default behaviour. The output will be named
+*NAME***.spell-marker.data** in the directory **WORK_DIRECTORY/*NAME*.cache**.
+
 
 **-O1**,**--output-one-point-prob**
 : Output the 1-point Parental Origin Probabilities. This will disable the output of the population data file
-unless -Op is also used.
+unless -Op is also explicitly used.
 
 # MARKER OBSERVATION FORMAT SPECIFICATION
 
@@ -174,4 +175,4 @@ encompasses.
 ~~~~
 # SEE ALSO
 
-`spell-pedigree` (1), `spell-qtl` (1).
\ No newline at end of file
+`spell-pedigree` (1), `spell-qtl` (1), `spell-qtl-examples` (1).
\ No newline at end of file

doc/man/spell-pedigree.1.md

@@ -8,7 +8,7 @@ spell-pedigree – Precompute the Markov Models for a pedigree
 
 # SYNOPSIS
 
-**spell-pedigree** [**-h**] [**-wd** *PATH*] [**-s** *CHAR*] **-p** *FILE*
+**spell-pedigree** [**-h**] [**--wd** *PATH*] **-n** *NAME* [**-s** *CHAR*] **-p** *FILE*
 
 # DESCRIPTION
 
@@ -18,6 +18,12 @@ pedigree.
 It outputs a data file that can be used with **spell-marker** to compute the Parental Origin
 Probabilities for this pedigree given allelic or genotype observations on a set of markers. 
 
+**-wd**,**--work-directory** *PATH*
+: Path to directory for cache files and outputs. Defaults to the **current directory**.
+
+**-n**,**--name** *NAME*
+: User-friendly name for this configuration
+
 **-p**, **--pedigree-file** *FILE*
 : Path to the genetic map file.
 
@@ -40,16 +46,13 @@ Probabilities for this pedigree given allelic or genotype observations on a set
 **-h**, **--help**
 : Display usage.
 
-**-wd**, **--work-directory** *PATH*
-: Path to directory for output files. Defaults to current directory.  
-
 **-s**,**--separator** *CHAR*
 : Column delimiter character used in the pedigree file. Defaults to ";".
 
 # OUTPUT
 
-**spell-pedigree** will create a file named *FILE***.ped-data** next to the input file.
+**spell-pedigree** will create a file named *NAME***.spell-pedigree.data** in the directory **WORK_DIRECTORY/*NAME*.cache**.
 
 # SEE ALSO
 
-`spell-marker` (1), `spell-qtl` (1).
\ No newline at end of file
+`spell-marker` (1), `spell-qtl` (1), `spell-qtl-examples` (1).
\ No newline at end of file

doc/man/spell-qtl-examples.1.md

+% SPELL-QTL-EXAMPLES(1) Spell-QTL software suite
+% Damien Leroux <damien.leroux@inra.fr>, Sylvain Jasson <sylvain.jasson@inra.fr>
+% December 2016
+
+# NAME
+
+spell-qtl-examples – Example datasets for the spell-qtl software suite.
+
+# DESCRIPTION
+
+The datasets are located in /usr/local/share/spell-qtl/examples if it was installed system-wide, or share/spell-qtl/examples
+in the installation directory.
+
+The example datasets each consist in a set of files :
+ - the pedigree in a **.ped** file,
+ - the genetic map in a **.map** file,
+ - one or more genotypic or allelic observation files in **.gen** files,
+ - one or more sets of trait observations in **.phen** files.
+
+Additionally, a **README** file in each directory describes the dataset features and the commands to run to process them.
+
+# SEE ALSO
+
+`spell-pedigree` (1), `spell-marker` (1), `spell-qtl` (1)
\ No newline at end of file

doc/man/spell-qtl.1.md

@@ -8,26 +8,29 @@ spell-qtl – Compute n-point Parental Origin Probabilities and perform QTL anal
 
 # SYNOPSIS
 
-**spell-qtl** [*options...*] **-n** *NAME* **-gm** *MAP* **-p** *POPDATA* *GEN* *TRAITS* [**-p**...]  [model and algorithms configuration...]
+**spell-qtl** [*options...*] [**--wd** *PATH*] **-n** *NAME* **-gm** *MAP* **-p** *POPDATA* *GEN* *TRAITS* [**-p**...] [model and algorithms configuration...]
 
 # DESCRIPTION
 
 **spell-qtl** computes the n-point Parental Origin Probabilities along the linkage groups using the data provided by
 **spell-marker**.
 
+**spell-qtl** expects that **spell-pedigree** and **spell-marker** have been run beforehand with the same working directory and configuration name.
+
+**-wd**,**--work-directory** *PATH*
+: Path to directory for cache files and outputs. Defaults to the **current directory**.
+
 **-n**,**--name** *NAME*
 : User-friendly name for this configuration
 
 **-gm**,**--genetic-map** *MAP*
 : Path to the genetic map file
 
-**-p**,**--population** *POPDATA* *GEN* *TRAITS*
+**-p**,**--population** *GEN* *TRAITS*
 : Specify a new population (dataset) to work on.
 
-    The *POPDATA* path must point to a file output by spell-marker. *GEN* is the name of the phenotyped generation.
-    The *TRAITS* path must point to a trait observation file with the **same** number of individuals as defined for
-    the given generation in the pedigree for this population.
-    The genetic map **MUST** be specified **BEFORE** any population data.
+    *GEN* is the name of the phenotyped generation. The *TRAITS* path must point to a trait observation file with the
+    **same** number of individuals as defined for the given generation in the pedigree for this population.
 
 # OPTIONS
 
@@ -42,9 +45,6 @@ spell-qtl – Compute n-point Parental Origin Probabilities and perform QTL anal
 **-N**,**--notes** *TEXT*
 : Optional free text
 
-**-wd**,**--work-directory** *PATH*
-: Path to directory for cache files and outputs. Defaults to **/tmp**.
-
 **-P**,**--parallel** *N_CORES*
 : Setup parallel computations (number of cores to use or 'auto'). Defaults to **0**.
 
@@ -62,6 +62,9 @@ Enabled by default only if output is on a terminal.
 
 The following configures the construction of the linear model.
 
+**output-nppop**
+: Compute the n-point Parental Origin Probabilities and exit. The results will be written under the **WORK_DIRECTORY/NAME.n-point** directory.
+
 **connected**
 : Select connected mode. Disabled by default.
 
@@ -123,4 +126,4 @@ The standard pipeline is:
 
 # SEE ALSO
 
-`spell-pedigree` (1), `spell-qtl` (1).
\ No newline at end of file
+`spell-pedigree` (1), `spell-qtl` (1), `spell-qtl-examples` (1).
\ No newline at end of file

examples/F3-outbred/F3-outbred.info

+2017-01-02 18:26:01.587360
+POP A 1
+POP F1 100
+POP C 1
+POP B 1
+POP D 1
+POP F3 1000
+POP F2 100
+POP CD 100
+POP AB 100
+QTL 104.61 1.64 52.56
+trait t1 qtl [('M_2_14', 104.61)] effect [{'a': 20.0, 'A': 20.0, 'c': 10.0, 'B': 30.0, 'd': 0.0, 'C': 10.0, 'b': 30.0, 'D': 0.0}] epistasis {} noise 1.0 0.0 1.0
+trait t3 qtl [('M_2_14', 104.61)] effect [{'a': 100.0, 'A': 100.0, 'c': 0.0, 'B': 10.0, 'd': 2000.0, 'C': 0.0, 'b': 10.0, 'D': 200.0}] epistasis {} noise 1.0 0.0 5.0
+trait t2 qtl [('M_2_9', 52.56)] effect [{'a': 5.0, 'A': 5.0, 'c': 6.0, 'B': 3.0, 'd': 4.0, 'C': 6.0, 'b': 3.0, 'D': 4.0}] epistasis {} noise 1.0 0.0 0.5

examples/F3-outbred/F3-outbred.map

+*ch1 19 M_1_1 4.42 M_1_3 21.65 M_1_4 2.15 M_1_5 6.58 M_1_6 0.49 M_1_7 6.38 M_1_8 6.01 M_1_9 11.35 M_1_10 11.1 M_1_11 9.74 M_1_12 8.35 M_1_13 4.88 M_1_14 3.11 M_1_15 8.93 M_1_16 15.7 M_1_17 20.61 M_1_18 0.65 M_1_19 7.9 M_1_20
+*ch2 15 M_2_1 4.39 M_2_2 3.01 M_2_3 1.83 M_2_4 3.7 M_2_5 6.12 M_2_6 9.33 M_2_7 3.25 M_2_8 22.21 M_2_10 8.01 M_2_11 33.01 M_2_12 3.47 M_2_13 12.18 M_2_15 2.91 M_2_16 6.58 M_2_17

examples/F3-outbred/commands

+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 -mt 4
+spell-qtl -n demo -wd spell/ -gm F3-outbred.map -p F3 F3-outbred_F3.phen -P auto QTL-detection CIM-

examples/F3-outbred/test_script.txt

+map,20|17,150|120,0|0
+lineobs,A,aA,aa:0 AA:2
+lineobs,B,bB,bb:0 BB:2
+lineobs,C,cC,cc:0 CC:2
+lineobs,D,dD,dd:0 DD:2
+cross,AB,A,B,100,None
+cross,CD,C,D,100,None
+cross,F1,AB,CD,100,None
+self,F2,F1,100,None
+self,F3,F2,1000,aa:0 ab:0 ac:0 ad:0 Aa:1 Ab:1 Ac:1 Ad:1 ba:0 bb:0 bc:0 bd:0 Ba:1 Bb:1 Bc:1 Bd:1 ca:0 cb:0 cc:0 cd:0 Ca:1 Cb:1 Cc:1 Cd:1 da:0 db:0 dc:0 dd:0 Da:1 Db:1 Dc:1 Dd:1 aA:1 aB:1 aC:1 aD:1 AA:2 AB:2 AC:2 AD:2 bA:1 bB:1 bC:1 bD:1 BA:2 BB:2 BC:2 BD:2 cA:1 cB:1 cC:1 cD:1 CA:2 CB:2 CC:2 CD:2 dA:1 dB:1 dC:1 dD:1 DA:2 DB:2 DC:2 DD:2
+qtls,3
+trait,t1,F3,1,a:20 A:20 b:30 B:30 c:10 C:10 d:0 D:0,None,1,0,1
+trait,t2,F3,1,a:5 A:5 b:3 B:3 c:6 C:6 d:4 D:4,None,1,0,.5
+trait,t3,F3,1,a:100 A:100 b:10 B:10 c:0 C:0 d:2000 D:200,None,1,0,5

examples/three_parents_F2/commands

+spell-pedigree -wd spell/ -n toto -p example1.ped
+spell-marker -n toto -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 connected -P auto

examples/three_parents_F2/example1.info

+2017-01-01 15:57:03.161723
+POP A 1
+POP F1 1
+POP C 1
+POP B 1
+POP F1C 1
+POP F2 100
+POP F2C 100
+QTL 123.28 142.46
+trait t1 qtl [('M_1_16', 123.28), ('M_1_19', 142.46)] effect [{'a': 2.0, 'c': -1.0}, {'a': 3.0, 'c': -2.0}] epistasis {} noise 1.0 0.0 2.0
+trait t1 qtl [('M_1_19', 142.46), ('M_1_16', 123.28)] effect [{'a': 2.0, 'b': 0.0}, {'a': 3.0, 'b': 0.0}] epistasis {} noise 1.0 0.0 1.0

examples/three_parents_F2/example1.map

+*ch1 18 M_1_1 7.69 M_1_2 11.26 M_1_3 9.18 M_1_4 10.86 M_1_5 0.91 M_1_6 11.68 M_1_7 16.79 M_1_8 12.94 M_1_9 4.43 M_1_10 4.51 M_1_11 0.0 M_1_12 6.94 M_1_13 17.77 M_1_14 2.49 M_1_15 6.68 M_1_17 0.21 M_1_18 25.66 M_1_20
+*ch2 17 M_2_1 4.65 M_2_2 1.46 M_2_3 9.24 M_2_4 0.71 M_2_5 18.73 M_2_6 3.86 M_2_7 15.5 M_2_8 17.31 M_2_9 2.1 M_2_10 9.96 M_2_11 3.34 M_2_12 9.05 M_2_13 16.94 M_2_14 1.71 M_2_15 4.8 M_2_16 0.64 M_2_17

examples/three_parents_F2/example1.ped

+generation;individual;mother;father
+A;1;0;0
+B;2;0;0
+C;3;0;0
+F1;4;1;2
+F1C;5;1;3
+F2;6;4;4
+F2;7;4;4
+F2;8;4;4
+F2;9;4;4
+F2;10;4;4
+F2;11;4;4
+F2;12;4;4
+F2;13;4;4
+F2;14;4;4
+F2;15;4;4
+F2;16;4;4
+F2;17;4;4
+F2;18;4;4
+F2;19;4;4
+F2;20;4;4
+F2;21;4;4
+F2;22;4;4
+F2;23;4;4
+F2;24;4;4
+F2;25;4;4
+F2;26;4;4
+F2;27;4;4
+F2;28;4;4
+F2;29;4;4
+F2;30;4;4
+F2;31;4;4
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+F2;34;4;4
+F2;35;4;4
+F2;36;4;4
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+F2;39;4;4
+F2;40;4;4
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+F2C;202;5;5
+F2C;203;5;5
+F2C;204;5;5
+F2C;205;5;5

examples/three_parents_F2/example1_F2.gen

+data type F2
+100 37 0 0
+*M_1_1 HHBHHHHAHHAAHAABHAAHABHBBABAHAHHAHHHHAAHHHHHHHHB-HHAHHABABHAABB-HHHHHHAABAHHHAHHH-AHHHHAHAHBBHBHAHHH
+*M_1_2 HHBHHHHAHHHAHAABHAABABHHBABAHAHHAHAHHAAAHHHHHHABBHHHHHABAHHHAHHHHHHHHHHABAHHHHBHHBAHHHHAHAHHBABHHHHH
+*M_1_3 HAHHHHBAHBHAHAHBHAABAHHHBABAHAHHAAAHHAAAHAHHHHHBHHHBHHHBAHHAAHHBHAHHHHA-BAHBHBAHHBAHHHHHAAHHBABBAHHH
+*M_1_4 HHHHHHBAHBHAAAHBHAAHHBHH-ABHHHH-AHAHHAAAHAHHHBHBHHABHHHBHHHAAHHHHAHHBHAABABBHBHHHBAHHHHAAAHHHAB-AHHH
+*M_1_5 HHH-AH-HHBHAAAHBHAAHHBHHB-BHHBHHAHAAAHHHHHBHHBHH-HABHHHBHHHAAHHHHAHH-HAABHBHHBHHHBHHHHBAAAHA-AHBAHHH
+*M_1_6 HHHHAHHHHBHAAAHBHAAHHBHHBABHHBHHAHAAAHHHHHBHHB-HHHABHHHBHHHAAHHHHAHHBHAABHBHHBHHHBHHHHBAAAHABAHBAHHH
+*M_1_7 HHHHH-HHHBHHAAHBHHHHABA-BABHHBBHHBAAAHHHHHHHHBAHHBABAHHBHHHAAHHHHAHHBAAAHHBHHBHHHBBHHHBAHAHAHAHBAHHH
+*M_1_8 HHBHHHHHHBHHAHHHHHHHHHAHHABHHBHBHHAAHHHHHHHHHBAHBHABAHHHHAHAAHHAHAHHBAHHAABHHHAHABBHBBBAHAHHHAAHAAHH
+*M_1_9 HHBBHHHHHBHBAAHH-HHHHAAHHABAHBHBHHAAHHHHHHHHHBHHBAABHHAHHAAAHHHAHAHABHHHAABAHHAAABBHBBHHHAHHHAAHAAHH
+*M_1_10 HHBBHAHHHBHBAAHHHHHHHAAHHAHAHBHBHHHAAHHHHHHBHBHHBAABHHHHHAAAHHHAHAHABHHHAABABHAAABBHBBHHHHHHHAAHAAHH
+*M_1_11 HHBBHAHHHBHBAAAHHHHHHAAHHABAHHHHHHHAAHHHHHHBHBHHBAABHHHHHAAAHHHAHHHABHHHAABABHAAABBHBBHHH-HHHAAHAAHH
+*M_1_12 HHBBHAHHHBHBAAAHHHHHHAAHHABAHHHHHHHAAHHHHHHBHBHHBAABHHHHHAAAHHHAHHH-BHHHAABABHAAABBHBB-HHHHHHAAHAAHH
+*M_1_13 HBBBHAHHHBHBAAHHHHHHHAAHHABAHHHHHHHAAHHHAHHBHBHHBAABHHHHHAAAHAHHHHHABHHHAABHHHAAHBHHBBHHHHHHBHAAAAHA
+*M_1_14 HHBHHAHHHBHBAAHHHHHAHHAHH-AHBAHHHBHAHHHHAHHBHABHHAABHBHHHAAAHAHHHABHBHBHAHB-HHAHHBHHBHHHHAHBHHAAAAHH
+*M_1_15 HHBHHAHHHBHBAAHHHHH-HHAHHAAHBAHHH-HAHHHHAHABHABHHAABHBHHHHAAHAH-HABHBHHHAH-HHHAHHBHHBHHHH-HHHHAAA-HH
+*M_1_16 HHHHHAHHA-HBAAHHHHHAHHAHHAAHBAHHHBHAHAHHABABHABHHAABHBHHHHAAHAHHHABHBHHHABBAHBAHHBHHBHHHHAHHHHAHAAHH
+*M_1_17 HHHHHAHHABHB-AHHHHHAHHAHHAAHBAHHHBHAHAHHABABHABHHAABH-HHHHAAHA-HHABHBHHHABBAHBAHHBHHBHHHHAHHHHAHAAHH
+*M_1_18 HHHHHAHHABHBAAHHHHHAHHAH-AAHBAHHHBHAHA-HABABHABHHAABHBHHHHAAHAHHHABHBHHHABBAHBAHHBHHBHHHHAHHHHAHAAHH
+*M_1_19 HBHHHHHHABBBAHHHHHHAHHHHHAABBAHHHBBHHAHAABHBHABHHAHHHBHHHHAAHABHH-BHBHHBAAHHHBAHHBHBHHAHHHHHHHHHAHHA
+*M_1_20 HBHHHHHAHBHBAAHHHBHAHHH-AAAB-AHHHBB-HAHAABHBHAHHHAHHHBHHBHAHAABHHHBHBHHHAHHAHHAHABHBHHAHHHHHHABHAHHA
+*M_2_1 BHHHBHHHHHBAAHHHBABH-ABBBHHBHHBAAABHHABHBHBHHBHHHHABBBAHHBHAAHHHHBHHHAHAAAAAHHBHBHHAHBAHAABHBAHHHAHB
+*M_2_2 HHHHBHHHHHBAAHHHBABHAABBHHHBHHBAAABHHAHHBHHHHBHH-H-BBBAHHBAAABHHBBHHHAHAAAAAHH-HBHHAHBAHAABHBABHHAHB
+*M_2_3 HHBHBH-HHHBAAHHHB-BHAABBHHHBHHBAAAB-HAHHBHHHHBHHHHABBBAHHBAAA-HHBBHHHAHAAAAAHHBHBHHAHBAHAABHBABHHAHB
+*M_2_4 HABHBHBHHHBAHAHHBAHHAAHBHHHBHHBAAAHHAHH-BHHHHBBABAHHBHHHHBAAABHHBBHHHAHAAAAAHBBHBHHAHBH-AABBBABAHAHB
+*M_2_5 HABHB-BHHHBAHAHHBAHHAAHBHHHBHHBAAAHHAHHHBHHHHB-ABAHBBHHHHBAAABHHBBHHHAHAAAAAHBBHBHHAHHH-AABBBABAHAHB
+*M_2_6 HAHABHHHHAHAHAHBBHHBHABBHHHBHHBBAAAAAHAHBHHHHHAABHHH-HBHHBHAABBABHHHBHHAAAAAHBBHBAHHHAHHAABBHABAHAHB
+*M_2_7 HAH-BHBHHAHAHAHBHHHBHABBHH-BHHBBAAAAAHAHBHHHHB-ABHHHBHBHHBHAABBABHHHBHHAAHHAHBBHBAHHBAH-HABBHHBAHAHB
+*M_2_8 HAHAHABHHAAAHAHBAAHBHABBHHHBA-BBAHAAAHHHBHHHHBHHBAHAB-BHHBHA-BBABHHHB-HAAHAAHABHBAAHBAHHHABBAHBA-AH-
+*M_2_9 AHHAHABHHAAHHHHBAAHBHA-BHBH-AHHHAH-AHHAHBHAHBBHHBA-ABHBHHBHAABBABHABBHBAHHAHHAB-BHHAHAHHHABBABBABAHB
+*M_2_10 AHAAHABHHAAHHHBBAAHBHABBHBHBAHHHAHBAHAAHBHAH-BHHBABABHBHHBHHA--ABHABBHBAHAAHHABHBHHAHAHHHABBABBABAHB
+*M_2_11 AHAAHA-HHAAHHHBBAAHBHAHBHBHBHBHAAH-AHAAHB-AHBBHHHABABHBAHBBHABBABH-BBHBHHAAAAHBHH-HAHAHHAABHABBABAHH
+*M_2_12 AHAAHAHHHAAHHHHBA-HBAAHBHBHBHBHAAHBAHAAHBHAHBBHHHABABHBAHBHHABBABHABBHBHHAAAAHBHHHHAHAHHAABHABBABAHH
+*M_2_13 AHAAHAAHHAAHHAHBAABHHAHBHBHHHBHAAHHAHAAHBBAHHBHBHABHB-BA-BHHABBABHABBHHHHAHAAHBHHHHBHAHHAABHAHBAB-AA
+*M_2_14 ABAAHHAHHAAHHAHBAABHAHHHHBHBBBHAAHAAHAHABBAHHBHHHHBHBBHAHBHHHBBHBHABHHHBBHHABHBHHHHBHHHH-AHAHBHABAAA
+*M_2_15 ABAAHHAHHAAHHAHBAABHAHHHHBHBBBHAAHAAHAHABBAHHBHHHHBHBBHAHBAHHBBHHHABHHHBBHHABHBH-HHBHHHHAAHAHBHABAAA
+*M_2_16 ABAAHHAHHAAHHAHBAABHAHHHHBHBBBHAAHHAHHHABBAHHBHHHHBBBB-AHBAHHBBHHBABHHHBBHHABHBHHHHBAHHHAAHAHBHABAAA
+*M_2_17 ABAAHHAHHAAHHAHBAABHAHHHHBHBBBAAAHHAHHHABBAHHBHHHHBBBBHAHBAHHBBHHBABHHHBBHHABABHHHHBAHHHAAHAHBHABAAA

examples/three_parents_F2/example1_F2.phen

+*t1 6.64860236836 4.48333766263 4.63945285025 4.76820197025 3.98475100377 7.7907636621 5.91623439645 3.34720741877 9.83405150226 -0.989276901108 2.85343753808 -0.452357427443 8.76926205797 8.73132087324 4.65962311312 4.62082330631 6.38653985804 4.989734855 4.28878631848 9.58223131681 5.36736423952 4.09469337742 7.92026671011 6.2855833754 3.75750777254 10.4304960767 11.5971147199 0.182921433465 -0.995052015451 10.333467377 5.10418651709 5.9164712845 4.66692732168 -0.962300148092 2.19979965366 9.35671579545 7.0948711129 10.0074456425 4.21066483587 6.52910034897 11.1193797151 0.136086581615 8.81773633071 -1.57335016648 5.47797407498 9.1689437749 1.6015919434 5.49533371363 5.70493918579 8.97894226651 9.61494699886 0.66729239529 6.68862822927 -1.70409103605 6.39794906648 6.25386383503 4.4817775051 4.3568018895 10.9461738855 9.73913793381 4.58160317351 9.67054859487 3.11563958805 4.86338634788 6.31047327314 8.92722186248 0.814254956503 6.74247632594 1.30741471213 5.31580476866 5.52796983437 3.01218646102 9.80427453273 3.96487115813 2.70931590757 6.50630409545 6.59223986179 1.01886549119 10.0882965697 4.32005434621 5.57877866525 -0.268758302975 5.61507629822 3.62224496753 0.909063757226 6.5575113055 8.11632733703 6.48570865845 6.28155082862 5.59834611728 5.1061983005 5.11895093067 4.02242496181 4.78061996178 6.79586348523 5.8755684148 9.7179662852 8.92181728966 2.87411208157 7.23454993645

examples/three_parents_F2/example1_F2C.gen

+data type F2C
+100 37 0 0
+*M_1_1 HHBBBAHABBBBAHBBHBHHAHBHBBBABHHHHAHHHHAHBHAHHAAHAAAH-AHAHBHHHHHHHHBBHAHAHHHHBHHHABBBHAAHHBHHHBAAHHHA
+*M_1_2 HABBBAHAHBBBAAHBHBHHA--HBBHABHHHHAHHHHAHHHAHHAABAAAHBAH-HBHHHHHHHHBBHAHAHHHHBHHBABBBHHAHHBHHH-AAAHAA
+*M_1_3 HABBBAHHHBBBAAHBHBHHAHH-HB-HBBHHHAHHHBAHAHAHBAABAHAHBAHAHBHAHHHAHHBBHABAHHHHBHBBABBBHHAHHBHHHBAA-HAA
+*M_1_4 AABBBAHHHBBHAHHB-BHBAHHHHBBHBBHHHAHHHBAHAHAHBAABAHAHBH-AHBAAAHHAHHB-HABAAHHHBHHBABBBHHAHHBHHHBAAAHAA
+*M_1_5 AABHBAHAHBBHAHHBHBHHAHHHHBBHHBABHHAHHBAB-HAHBAHBAHAHBBHABBAAAHHAHHBHHABAABBHHHHBABBBHHHHHBHAHBHHAAAH
+*M_1_6 AABHBAHAHBBHAHHBHBHHAHHHHBBHHBABHHAHHBABAHAHBAHBAHAHBBHABBAAAHHAHHBHHABAABBHHHHBABBBHHHHHBHA-BHHAAAH
+*M_1_7 HABHHH-HHBBHAHHBHBHHHHHHHBBHBBAHHHAHHBABAHAHBAHBAHAHBBHAHBAAAHHAHHBHHABAABBHHHHHAHBBHHHHHBHABBHHAAHH
+*M_1_8 HHHHHBHHHHBHAHHHHBHHHHHBHBBHHAHHAHAHHBABABAABAHHHHABBBHAHBAAAHBAHHBBAAHAABBAHHHBAHHBHAHHHBHABHHHAHBH
+*M_1_9 BHHHHHHHHHHHHHHHAHHHHH-HHBBBHHAHAHHHHBABAHAAHHHHHHABH-BAHBAAAHBAHHBHAAHAAHBAHHHHAHHBHAHHHBBABBHHAHBA
+*M_1_10 BH-HBHHBHHHHHHHHAHHHHHHAHBBBHHAHAHHHHBABAHHAHHHHHHAHHBBAHBAAAHBAHHBHAAHAAHHAHHHHAH-BAAHHHBBABBHHAHBH
+*M_1_11 HAHHBHHBHHHHHHHHHHHHHHHAHBBBHAAHAHHHHBABAHHAH-HBHHHHHBBAA-AAAHBAHHB-AAHAAHHAHAHHAHHBAAHHHBBABBHBAHBH
+*M_1_12 HAHHBHHBH-HHHHHHHHHHHHHAHBBBHAAH-HHHHBABAHHAHHHBHHHHHBBAABAAAHBAHHBHAAHAAHHAHAHHAHHBAAHHHBBABBHBAHBH
+*M_1_13 HAHHBBHBH-HHHBAHHHHHHBHAHBBHH-AHAHHHHBABAHHAHHHBHHHHHBBAABAAAHBABHBHAAHAHHAAHAHHAHAHAAHHBBBABBHBHHHH
+*M_1_14 HHHHHBHBAHHAHHABHHHHHBHAHBBHHAAAHHBHHHHB-HHAHHHAAHHHHHBHABHHAHBAHBBHAAHAHHHAHHHHHHAHAAHHHBBABHHBHHHH
+*M_1_15 HHHHHBHBABAAHHAHHHH-HBHAHBBHHAAAHHBHHHHBAHH-HHHAAHHHHHBHABHHAHBAHBBHAAHAHHHAHHHBHHABA-HHHBBABHHBHHHH
+*M_1_16 HHHHHBH-ABAHHHAHHHHHHBHAHBBHHAAAHHBHHHHBAHHAHHH-AHHHHHB-ABBHAABAHHBHAA-AHBBAHHHBBHABAAHHHBBAHHHBHBHB
+*M_1_17 HHHHHBHBABAHHHAHHHHHHBHAHBBHHAAAHHBHHHHBAHHAHHHHAHHHHHBHABBHA-BAHHBHAAHAHBBAHHHBHHABAAHHHBBAHHHBHBHB
+*M_1_18 HHHHHBHBA-AHHHAHHHHHHBH-HBBHHAAAHHBHHHHBAHHAHHHHAHHHHHBHABBHAA-AHHBHAAHAH-BAH-HBHHABAAHHHB-AHHHBHBHB
+*M_1_19 HHHHBBHBABABHHABHHHHHBHHHBBBHAAAHHBHHBBBAHHAHHHBAHAAHHBBHHHBAABAHHHHAHAAABHAHAHHHAHBAAH-HBBAHHHHBHHB
+*M_1_20 HHBBBBHBA-ABHHABH-HHHBHHHBBBHAAHHHBHHBBBAHHAHHHBAHHHHHBBHHHBHABAHHAHHHAAABHAHAHHHAHBAAHHBBBAHHHHBHHB
+*M_2_1 AHAHBHB-BAHHAA--BHBHBBBAABHHAHHHBBHAHHHHBBBHHAAABHBHAAHAHHHABHHHBBBHHBABABHBH--HHBAAHHHHAHHAHHHAHBAH
+*M_2_2 AHABBHABBAHHAAHHHABHBBBAABH-AHHHBBHAHHHHBBBHHAAABHBHAAAAHAHAH-HHBBBHHBABABHBHBAHHBAAHHHHAHHAHHHAHBAH
+*M_2_3 -HABBHABBAHHAABHHABHBBBAABHHAHHHBBHAHHHHBBHHHAAA-HBHAAAAHAHAHHHHBBBHHBABABHBHHAHHBAAHHHHAHHAHHHAHBAH
+*M_2_4 HHHBHAABBHHHA-BHHABHBHBHABHHAHHHBB-ABBHHBBHHHAAABHBHAHAAHHHAHAHHBB-AAH-BABHBHHAHHBAAHHHHAAHAHHHAHBA-
+*M_2_5 HHHBHAABBHHHAABHHABHBHBHABHHAHHHBBHABBHHBBHHHAAABHBHAHAAHHHAHAHHBBBAAHABABHBHHAHHBAAHHHHAAHHHHHAHBAH
+*M_2_6 AHBBBBABBHHHHAHHHHHHHBHHAHHHA-HAHBHAHBBHBBHHHHAHBHBAAHAABHHAHAHABHBAHAABAHHBHBHHHHHAHHABAAHHHHHAABAH
+*M_2_7 AHBBBBABBHHHHAHHHHHHHBHHABHHAHHABBHAHBBHBB-HHHAHBBBAAHAABHHAHAHABHBAHAABAHHBHBHHHHHHHHHBAAHHHBHAABAH
+*M_2_8 H-HBBBABHHHAHAHHHHHHHHBAABBBAHHAHHHHABBHB-HHBHAHBBBAHBAAB-HAHHHABHBABA-BAHHBHBHBHAH-AAHBHAHHHBHAABAH
+*M_2_9 ABHHHHABHHHAHAHHHHHH-HBAAHHAAAHAHBHHABBBBBHHBHAHHBHAHBAABHHAHHBABBHAHAHBHHHHHHHBHABHAAAHAHHHHBHAABAB
+*M_2_10 ABHHHHABHHHAHAH-HHHHHHBAAHHAAAHAHBHHABBBHBHHBHAHHHHHHBAABHAAHHBABBHAHAHBHHHHHHHBHABHAAAHAHH-HBHAABAB
+*M_2_11 HBHHAHABHHHAHAHHBHHHHHHAAHHAAAHHBBHHAB-BHHHHBHAAHHHHHBAAHHAHHHBBBBHHHHHBHHHHHHHB-AHHAAAHHHAHBB-AHBA-
+*M_2_12 HBHHAHABHHHAHAHHBHHHHHHAAHHAAAHHBBHHABBBAHHHBHAAHHHHHBAAHHAHHHBBBBHAHH-BHHHHHHHBHAHHAHAHHAAHBBAAHBAB
+*M_2_13 HB-HAHHBHHHAHAHBBHHHHHHAAHBAAAHABBHHHBBBAHHHBHAAHHHAHBAAHHABHHBBBHHAHHHBHHHHHHHBAHHAAHAHHAAHB-AAHBAB
+*M_2_14 HBAHABHBHHHHHAABHBAHHHHAAHBABAHAHBBHBHBHAAH-BHAAHHHHBBAAHAABHHHBBBHABHABHAAHAH-HAHHAAHHHHHAHBHAAAHAB
+*M_2_15 HBAHAHHBHHHHHAABHBAHHHAAAHBABAHAHBBHBHBHAAHHBHAAHHHHBBAAHAABHHHBBBHABHABHAAHAHHHAHHAAHHHHHAHBHAAAHAB
+*M_2_16 HBAHAHHBHHHHHAABB-AHHHAAA-BABAHAHBBHBHBHAAHHBHAAHHHHBBAABAABHHHBHBHABHABHAAHAHHHAHHHAHHHHHAHBHAAAHAH
+*M_2_17 HBAHAHHBHHHHHAABBHAHHHAAAHBABAHAHBB-BHBHAAHHBHAAHHHHBBAABAABHHHBHBHABHABHAHHAHHHAHHHAHHHHHAHHHAAAHAH

examples/three_parents_F2/example1_F2C.phen

+*t1 0.328355199448 5.10683118086 4.25659094776 4.68006179362 -0.913961759077 -5.74056021129 2.5774421982 -5.42063924828 14.0848049852 -2.63927222824 10.5477757029 -2.68675140521 3.7405394636 3.776776543 11.7206589206 -3.7989261696 2.44969980308 0.336531678083 0.708879219342 -1.17634659862 1.83688034735 -5.12092173165 -0.855333649927 2.29682472167 8.94916751201 -3.6974125265 -5.03705482099 -5.09062120779 -0.896108061832 11.3012069808 10.7769479288 13.3044122964 3.93518231088 1.7690759712 -4.48002172763 5.64254022097 4.37933766232 -0.21018452173 -2.57721074196 -5.63276033104 8.37708039457 2.5540940644 0.826562238715 10.6685299467 4.60193366912 0.598827798427 -0.529916605371 -2.74280507579 12.2432736343 1.468962466 6.32612546458 8.27854988619 5.63099942482 0.917998477715 -5.38207560287 -1.85768387876 4.56924607109 -2.33124087835 -1.06257007392 -3.62825533355 7.60734178979 9.78619130916 -8.35096725127 9.10903367186 -0.0468927916955 4.27775746703 1.76183412397 -2.48561806856 8.92519267479 7.80573629488 8.98780952553 8.47505730318 7.53615261543 -5.9435149851 -4.18000141774 11.2139889346 -1.04077912336 8.28298238534 0.155084812448 -2.02421875897 0.513853988638 6.88644989402 6.17801304882 -5.84501407477 11.145093232 12.4412439473 4.91184653193 -1.1463139581 0.666989612217 -3.12889876315 -7.04670755751 12.4323881661 4.70239774118 3.55258004496 3.17696862593 -0.769211208817 -1.31784172515 -1.07401601217 0.314941929721 -2.76645868474