merge upstream changes

.gitignore

@@ -1,2 +1 @@
-# OS specific ignore file
 .DS_Store

pyrat-data-single-mutation.csv → pyrat-data-1-mutation.csv

@@ -1,4 +1,4 @@
-ID,Line / Strain (Name),DOB,Father,Mother,Sacrifice reason,Mutation 1,Grade 1,Mutation 2,Grade 2,Mutation 3,Grade 3,Father: Mutation 1,Father: Grade 1,Father: Mutation 2,Father: Grade 2,Father: Mutation 3,Father: Grade 3,Mother: Mutation 1,Mother: Grade 1,Mother: Mutation 2,Mother: Grade 2,Mother: Mutation 3,Mother: Grade 3
+ID,Line / Strain (Name),DOB,Father 1,Mother 1,Sacrifice reason,Mutation 1,Grade 1,Mutation 2,Grade 2,Mutation 3,Grade 3,Father 1: Mutation 1,Father 1: Grade 1,Father 1: Mutation 2,Father 1: Grade 2,Father 1: Mutation 3,Father 1: Grade 3,Mother 1: Mutation 1,Mother 1: Grade 1,Mother 1: Mutation 2,Mother 1: Grade 2,Mother 1: Mutation 3,Mother 1: Grade 3
 ID-001,Line-A,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,het,,,,,Mut-A,wt,,,,,Mut-A,het,,,,
 ID-002,Line-A,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,wt,,,,,Mut-A,wt,,,,,Mut-A,het,,,,
 ID-003,Line-A,02/01/2026,ID-F1,ID-M1,End of experiment,Mut-A,het,,,,,Mut-A,wt,,,,,Mut-A,het,,,,

pyrat-data-2-mutations.csv

@@ -1,4 +1,4 @@
-ID,Line / Strain (Name),DOB,Father,Mother,Sacrifice reason,Mutation 1,Grade 1,Mutation 2,Grade 2,Mutation 3,Grade 3,Father: Mutation 1,Father: Grade 1,Father: Mutation 2,Father: Grade 2,Father: Mutation 3,Father: Grade 3,Mother: Mutation 1,Mother: Grade 1,Mother: Mutation 2,Mother: Grade 2,Mother: Mutation 3,Mother: Grade 3
+ID,Line / Strain (Name),DOB,Father 1,Mother 1,Sacrifice reason,Mutation 1,Grade 1,Mutation 2,Grade 2,Mutation 3,Grade 3,Father 1: Mutation 1,Father 1: Grade 1,Father 1: Mutation 2,Father 1: Grade 2,Father 1: Mutation 3,Father 1: Grade 3,Mother 1: Mutation 1,Mother 1: Grade 1,Mother 1: Mutation 2,Mother 1: Grade 2,Mother 1: Mutation 3,Mother 1: Grade 3
 ID-001,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,hom,Mut-B,hom,,,Mut-A,het,Mut-B,hom,,,Mut-A,hom,Mut-B,het,,
 ID-002,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,hom,Mut-B,hom,,,Mut-A,het,Mut-B,hom,,,Mut-A,hom,Mut-B,het,,
 ID-003,Line-AB,02/01/2025,ID-F1,ID-M1,End of experiment,Mut-A,het,Mut-B,hom,,,Mut-A,het,Mut-B,hom,,,Mut-A,hom,Mut-B,het,,

pyrat-data-3-mutations.csv

@@ -1,4 +1,4 @@
-ID,Line / Strain (Name),DOB,Father,Mother,Sacrifice reason,Mutation 1,Grade 1,Mutation 2,Grade 2,Mutation 3,Grade 3,Father: Mutation 1,Father: Grade 1,Father: Mutation 2,Father: Grade 2,Father: Mutation 3,Father: Grade 3,Mother: Mutation 1,Mother: Grade 1,Mother: Mutation 2,Mother: Grade 2,Mother: Mutation 3,Mother: Grade 3
+ID,Line / Strain (Name),DOB,Father 1,Mother 1,Sacrifice reason,Mutation 1,Grade 1,Mutation 2,Grade 2,Mutation 3,Grade 3,Father 1: Mutation 1,Father 1: Grade 1,Father 1: Mutation 2,Father 1: Grade 2,Father 1: Mutation 3,Father 1: Grade 3,Mother 1: Mutation 1,Mother 1: Grade 1,Mother 1: Mutation 2,Mother 1: Grade 2,Mother 1: Mutation 3,Mother 1: Grade 3
 ID-001,Line-ABC,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,het,Mut-B,wt,Mut-C,hom,Mut-A,wt,Mut-B,wt,Mut-C,het,Mut-A,het,Mut-B,het,Mut-C,het
 ID-002,Line-ABC,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,het,Mut-B,wt,Mut-C,hom,Mut-A,wt,Mut-B,wt,Mut-C,het,Mut-A,het,Mut-B,het,Mut-C,het
 ID-003,Line-ABC,02/01/2025,ID-F1,ID-M1,End of experiment,Mut-B,wt,Mut-A,het,Mut-C,hom,Mut-A,wt,Mut-B,wt,Mut-C,het,Mut-A,het,Mut-B,het,Mut-C,het

pyrat-data-forbidden-genotypes.csv

@@ -1,4 +1,4 @@
-ID,Line / Strain (Name),DOB,Father,Mother,Sacrifice reason,Mutation 1,Grade 1,Mutation 2,Grade 2,Mutation 3,Grade 3,Father: Mutation 1,Father: Grade 1,Father: Mutation 2,Father: Grade 2,Father: Mutation 3,Father: Grade 3,Mother: Mutation 1,Mother: Grade 1,Mother: Mutation 2,Mother: Grade 2,Mother: Mutation 3,Mother: Grade 3
+ID,Line / Strain (Name),DOB,Father 1,Mother 1,Sacrifice reason,Mutation 1,Grade 1,Mutation 2,Grade 2,Mutation 3,Grade 3,Father 1: Mutation 1,Father 1: Grade 1,Father 1: Mutation 2,Father 1: Grade 2,Father 1: Mutation 3,Father 1: Grade 3,Mother 1: Mutation 1,Mother 1: Grade 1,Mother 1: Mutation 2,Mother 1: Grade 2,Mother 1: Mutation 3,Mother 1: Grade 3
 ID-001,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,het,Mut-B,hom,,,Mut-A,hom,Mut-B,het,,,Mut-A,wt,Mut-B,hom,,
 ID-002,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,+,Mut-B,-,,,Mut-A,+,Mut-B,-,,,Mut-A,+,Mut-B,-,,
 ID-003,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,Tg,Mut-B,Tg,,,Mut-A,T,Mut-B,-,,,Mut-A,T,Mut-B,-,,

pyrat-data-forbidden-parents.csv

@@ -0,0 +1,7 @@
+ID,Line / Strain (Name),DOB,Father 1,Mother 1,Father 2,Mother 2,Sacrifice reason,Mutation 1,Grade 1,Father 1: Mutation 1,Father 1: Grade 1,Father 2: Mutation 1,Father 2: Grade 1,Mother 1: Mutation 1,Mother 1: Grade 1,Mother 2: Mutation 1,Mother 2: Grade 1
+ID-001,Line-A,15/12/2025,,,,,End of experiment,Mut-A,hom,,,,,,,,
+ID-002,Line-A,15/12/2025,ID-F1,,,,End of experiment,Mut-A,het,Mut-A,het,,,,,,
+ID-003,Line-A,02/01/2026,,,ID-M4,,End of experiment,Mut-A,het,,,Mut-A,het,,,,
+ID-004,Line-A,02/01/2026,,ID-M3,,ID-M4,End of experiment,Mut-A,het,,,,,Mut-A,het,Mut-A,het
+ID-005,Line-A,15/02/2026,ID-F5,,ID-F6,,End of experiment,Mut-A,hom,Mut-A,hom,Mut-A,hom,,,,
+ID-006,Line-A,15/12/2025,ID-F1,ID-M1,ID-F2,ID-M2,End of experiment,Mut-A,hom,Mut-A,hom,Mut-A,hom,Mut-A,het,Mut-A,het

pyrat-data-forbidden-schemes.csv

@@ -1,4 +1,4 @@
-ID,Line / Strain (Name),DOB,Father,Mother,Sacrifice reason,Mutation 1,Grade 1,Mutation 2,Grade 2,Mutation 3,Grade 3,Father: Mutation 1,Father: Grade 1,Father: Mutation 2,Father: Grade 2,Father: Mutation 3,Father: Grade 3,Mother: Mutation 1,Mother: Grade 1,Mother: Mutation 2,Mother: Grade 2,Mother: Mutation 3,Mother: Grade 3
+ID,Line / Strain (Name),DOB,Father 1,Mother 1,Sacrifice reason,Mutation 1,Grade 1,Mutation 2,Grade 2,Mutation 3,Grade 3,Father 1: Mutation 1,Father 1: Grade 1,Father 1: Mutation 2,Father 1: Grade 2,Father 1: Mutation 3,Father 1: Grade 3,Mother 1: Mutation 1,Mother 1: Grade 1,Mother 1: Mutation 2,Mother 1: Grade 2,Mother 1: Mutation 3,Mother 1: Grade 3
 ID-001,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,hom,Mut-B,hom,,,Mut-A,het,Mut-B,hom,,,Mut-A,hom,Mut-B,het,,
 ID-002,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,Mut-A,hom,Mut-B,hom,,,Mut-A,het,Mut-B,hom,,,Mut-A,hom,Mut-B,het,,
 ID-003,Line-AB,02/01/2025,ID-F1,ID-M1,End of experiment,Mut-A,het,Mut-B,hom,,,Mut-A,het,Mut-B,hom,,,Mut-A,hom,Mut-B,het,,

pyrat-data-multiple-parents-1-mutation.csv

@@ -0,0 +1,11 @@
+ID,Line / Strain (Name),DOB,Father 1,Mother 1,Father 2,Mother 2,Sacrifice reason,Mutation 1,Grade 1,Father 1: Mutation 1,Father 1: Grade 1,Father 2: Mutation 1,Father 2: Grade 1,Mother 1: Mutation 1,Mother 1: Grade 1,Mother 2: Mutation 1,Mother 2: Grade 1
+ID-001,Line-A,15/12/2025,ID-F1,ID-M1,ID-F2,ID-M2,End of experiment,Mut-A,hom,Mut-A,hom,Mut-A,hom,Mut-A,het,Mut-A,het
+ID-002,Line-A,15/12/2025,ID-F1,ID-M1,ID-F2,ID-M2,End of experiment,Mut-A,het,Mut-A,het,Mut-A,het,Mut-A,hom,Mut-A,hom
+ID-003,Line-A,02/01/2026,ID-F3,ID-M3,,ID-M4,End of experiment,Mut-A,het,Mut-A,hom,,,Mut-A,het,Mut-A,het
+ID-004,Line-A,02/01/2026,ID-F3,ID-M3,,ID-M4,End of experiment,Mut-A,hom,Mut-A,hom,,,Mut-A,het,Mut-A,wt
+ID-005,Line-A,15/02/2026,ID-F5,ID-M5,ID-F6,ID-M6,End of experiment,Mut-A,hom,Mut-A,hom,Mut-A,wt,Mut-A,hom,Mut-A,hom
+ID-006,Line-A,15/02/2026,ID-F5,ID-M5,ID-F6,ID-M6,End of experiment,Mut-A,wt,Mut-A,wt,Mut-A,wt,Mut-A,wt,Mut-A,wt
+ID-007,Line-A,15/02/2026,ID-F5,ID-M5,ID-F6,ID-M6,End of experiment,Mut-A,het,Mut-A,het,Mut-A,het,Mut-A,wt,Mut-A,wt
+ID-008,Line-A,15/03/2026,ID-F7,ID-M5,,ID-M8,End of experiment,Mut-A,het,Mut-A,hom,,,Mut-A,het,Mut-A,hom
+ID-009,Line-A,15/03/2026,ID-F7,ID-M5,,ID-M8,End of experiment,Mut-A,wt,Mut-A,hom,,,Mut-A,hom,Mut-A,hom
+ID-010,Line-A,15/03/2026,ID-F7,ID-M5,,ID-M8,End of experiment,Mut-A,hom,Mut-A,hom,,,Mut-A,hom,Mut-A,hom

pyrat-data-multiple-parents-2-mutations.csv

@@ -0,0 +1,11 @@
+ID,Line / Strain (Name),DOB,Father 1,Mother 1,Father 2,Mother 2,Sacrifice reason,Mutation 1,Grade 1,Mutation 2,Grade 2,Father 1: Mutation 1,Father 1: Grade 1,Father 1: Mutation 2,Father 1: Grade 2,Father 2: Mutation 1,Father 2: Grade 1,Father 2: Mutation 2,Father 2: Grade 2,Mother 1: Mutation 1,Mother 1: Grade 1,Mother 1: Mutation 2,Mother 1: Grade 2,Mother 2: Mutation 1,Mother 2: Grade 1,Mother 2: Mutation 2,Mother 2: Grade 2
+ID-001,Line-AB,15/12/2025,ID-F1,ID-M1,ID-F2,ID-M2,End of experiment,Mut-A,het,Mut-B,het,Mut-A,wt,Mut-B,het,Mut-A,wt,Mut-B,het,Mut-A,het,Mut-B,wt,Mut-A,het,Mut-B,wt
+ID-002,Line-AB,15/12/2025,ID-F1,ID-M1,ID-F2,ID-M2,End of experiment,Mut-A,hom,Mut-B,het,Mut-A,hom,Mut-B,wt,Mut-A,hom,Mut-B,wt,Mut-A,hom,Mut-B,het,Mut-A,hom,Mut-B,het
+ID-003,Line-AB,02/01/2026,ID-F3,ID-M3,ID-F4,,End of experiment,Mut-A,hom,Mut-B,het,Mut-A,hom,Mut-B,wt,Mut-A,wt,Mut-B,hom,Mut-A,het,Mut-B,het,,,,
+ID-004,Line-AB,02/01/2026,ID-F3,ID-M3,ID-F4,,End of experiment,Mut-A,het,Mut-B,het,Mut-A,hom,Mut-B,wt,Mut-A,hom,Mut-B,wt,Mut-A,het,Mut-B,het,,,,
+ID-005,Line-AB,15/02/2026,ID-F5,ID-M5,ID-F6,ID-M6,End of experiment,Mut-A,hom,Mut-B,het,Mut-A,hom,Mut-B,wt,Mut-A,wt,Mut-B,het,Mut-A,hom,Mut-B,het,Mut-A,hom,Mut-B,het
+ID-006,Line-AB,15/02/2026,ID-F5,ID-M5,ID-F6,ID-M6,End of experiment,Mut-A,hom,Mut-B,het,Mut-A,wt,Mut-B,het,Mut-A,wt,Mut-B,het,Mut-A,wt,Mut-B,het,Mut-A,wt,Mut-B,het
+ID-007,Line-AB,15/02/2026,ID-F5,ID-M5,ID-F6,ID-M6,End of experiment,Mut-A,het,Mut-B,wt,Mut-A,het,Mut-B,wt,Mut-A,het,Mut-B,wt,Mut-A,wt,Mut-B,wt,Mut-A,wt,Mut-B,wt
+ID-008,Line-AB,15/03/2026,ID-F7,ID-M5,,ID-M8,End of experiment,Mut-A,het,Mut-B,het,Mut-A,hom,Mut-B,wt,,,,,Mut-A,het,Mut-B,hom,Mut-A,wt,Mut-B,het
+ID-009,Line-AB,15/03/2026,ID-F7,ID-M5,,ID-M8,End of experiment,Mut-A,wt,Mut-B,hom,Mut-A,hom,Mut-B,wt,,,,,Mut-A,hom,Mut-B,hom,Mut-A,hom,Mut-B,hom
+ID-010,Line-AB,15/03/2026,ID-F7,ID-M5,,ID-M8,End of experiment,Mut-A,het,Mut-B,wt,Mut-A,het,Mut-B,het,,,,,Mut-A,het,Mut-B,wt,Mut-A,het,Mut-B,wt

pyrat-data-multiple-parents-3-mutations.csv

@@ -0,0 +1,12 @@
+ID,Line / Strain (Name),DOB,Father 1,Mother 1,Father 2,Mother 2,Sacrifice reason,Mutation 1,Grade 1,Mutation 2,Grade 2,Mutation 3,Grade 3,Father 1: Mutation 1,Father 1: Grade 1,Father 1: Mutation 2,Father 1: Grade 2,Father 1: Mutation 3,Father 1: Grade 3,Father 2: Mutation 1,Father 2: Grade 1,Father 2: Mutation 2,Father 2: Grade 2,Father 2: Mutation 3,Father 2: Grade 3,Mother 1: Mutation 1,Mother 1: Grade 1,Mother 1: Mutation 2,Mother 1: Grade 2,Mother 1: Mutation 3,Mother 1: Grade 3,Mother 2: Mutation 1,Mother 2: Grade 1,Mother 2: Mutation 2,Mother 2: Grade 2,Mother 2: Mutation 3,Mother 2: Grade 3
+ID-001,Line-ABC,15/12/2025,ID-F1,ID-M1,ID-F2,ID-M2,End of experiment,Mut-A,wt,Mut-B,wt,Mut-C,hom,Mut-A,wt,Mut-B,wt,Mut-C,het,Mut-A,wt,Mut-B,wt,Mut-C,het,Mut-A,het,Mut-B,het,Mut-C,het,Mut-A,het,Mut-B,het,Mut-C,het
+ID-002,Line-ABC,15/12/2025,ID-F1,ID-M1,ID-F2,ID-M2,End of experiment,Mut-A,hom,Mut-B,wt,Mut-C,wt,Mut-A,het,Mut-B,het,Mut-C,het,Mut-A,het,Mut-B,het,Mut-C,het,Mut-A,hom,Mut-B,wt,Mut-C,het,Mut-A,hom,Mut-B,wt,Mut-C,het
+ID-003,Line-ABC,02/01/2026,ID-F3,ID-M3,,ID-M4,End of experiment,Mut-A,het,Mut-B,het,Mut-C,het,Mut-A,het,Mut-B,het,Mut-C,het,,,,,,,Mut-A,wt,Mut-B,het,Mut-C,het,Mut-A,wt,Mut-B,het,Mut-C,het
+ID-004,Line-ABC,02/01/2026,ID-F3,ID-M3,,ID-M4,End of experiment,Mut-A,het,Mut-B,hom,Mut-C,het,Mut-A,het,Mut-B,hom,Mut-C,wt,,,,,,,Mut-A,wt,Mut-B,het,Mut-C,hom,Mut-A,wt,Mut-B,het,Mut-C,hom
+ID-005,Line-ABC,15/02/2026,ID-F5,ID-M5,ID-F6,ID-M6,End of experiment,Mut-A,hom,Mut-B,wt,Mut-C,het,Mut-A,hom,Mut-B,wt,Mut-C,wt,Mut-A,wt,Mut-B,het,Mut-C,het,Mut-A,hom,Mut-B,het,Mut-C,hom,Mut-A,hom,Mut-B,wt,Mut-C,het
+ID-006,Line-ABC,15/02/2026,ID-F5,ID-M5,ID-F6,ID-M6,End of experiment,Mut-A,het,Mut-B,het,Mut-C,hom,Mut-A,wt,Mut-B,wt,Mut-C,wt,Mut-A,wt,Mut-B,wt,Mut-C,wt,Mut-A,wt,Mut-B,hom,Mut-C,wt,Mut-A,wt,Mut-B,hom,Mut-C,wt
+ID-007,Line-ABC,15/02/2026,ID-F5,ID-M5,ID-F6,ID-M6,End of experiment,Mut-A,het,Mut-B,wt,Mut-C,wt,Mut-A,het,Mut-B,wt,Mut-C,wt,Mut-A,het,Mut-B,wt,Mut-C,wt,Mut-A,wt,Mut-B,wt,Mut-C,wt,Mut-A,wt,Mut-B,wt,Mut-C,wt
+ID-008,Line-ABC,15/03/2026,ID-F7,ID-M5,,ID-M8,End of experiment,Mut-A,het,Mut-B,het,Mut-C,het,Mut-A,hom,Mut-B,wt,Mut-C,hom,,,,,,,Mut-A,het,Mut-B,hom,Mut-C,wt,Mut-A,wt,Mut-B,het,Mut-C,hom
+ID-009,Line-ABC,15/03/2026,ID-F7,ID-M5,,ID-M8,End of experiment,Mut-A,wt,Mut-B,hom,Mut-C,hom,Mut-A,hom,Mut-B,wt,Mut-C,hom,,,,,,,Mut-A,hom,Mut-B,het,Mut-C,hom,Mut-A,hom,Mut-B,het,Mut-C,hom
+ID-010,Line-ABC,15/03/2026,ID-F7,ID-M5,,ID-M8,End of experiment,Mut-A,het,Mut-B,wt,Mut-C,hom,Mut-A,het,Mut-B,wt,Mut-C,hom,,,,,,,Mut-A,wt,Mut-B,wt,Mut-C,hom,Mut-A,wt,Mut-B,wt,Mut-C,hom
+

standardised-data-single-mutation.csv → standardised-data-1-mutation.csv

@@ -1,4 +1,4 @@
-ID_offspring,line_name,date_of_birth,ID_father,ID_mother,sacrifice_reason,n_mutations,mutation_1,genotype_offspring,genotype_father,genotype_mother
+ID_offspring,line_name,date_of_birth,ID_father_1,ID_mother_1,sacrifice_reason,n_mutations,mutation_1,genotype_offspring,genotype_father,genotype_mother
 ID-001,Line-A,15/12/2025,ID-F1,ID-M1,End of experiment,1,Mut-A,het,wt,het
 ID-002,Line-A,15/12/2025,ID-F1,ID-M1,End of experiment,1,Mut-A,wt,wt,het
 ID-003,Line-A,02/01/2026,ID-F1,ID-M1,End of experiment,1,Mut-A,het,wt,het

standardised-data-2-mutations.csv

@@ -1,4 +1,4 @@
-ID_offspring,line_name,date_of_birth,ID_father,ID_mother,sacrifice_reason,n_mutations,mutation_1,mutation_2,genotype_offspring,genotype_father,genotype_mother
+ID_offspring,line_name,date_of_birth,ID_father_1,ID_mother_1,sacrifice_reason,n_mutations,mutation_1,mutation_2,genotype_offspring,genotype_father,genotype_mother
 ID-001,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,2,Mut-A,Mut-B,hom_hom,het_hom,hom_het
 ID-002,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,2,Mut-A,Mut-B,hom_hom,het_hom,hom_het
 ID-003,Line-AB,02/01/2025,ID-F1,ID-M1,End of experiment,2,Mut-A,Mut-B,het_hom,het_hom,hom_het

standardised-data-3-mutations.csv

@@ -1,4 +1,4 @@
-ID_offspring,line_name,date_of_birth,ID_father,ID_mother,sacrifice_reason,n_mutations,mutation_1,mutation_2,mutation_3,genotype_offspring,genotype_father,genotype_mother
+ID_offspring,line_name,date_of_birth,ID_father_1,ID_mother_1,sacrifice_reason,n_mutations,mutation_1,mutation_2,mutation_3,genotype_offspring,genotype_father,genotype_mother
 ID-001,Line-ABC,15/12/2025,ID-F1,ID-M1,End of experiment,3,Mut-A,Mut-B,Mut-C,het_wt_hom,wt_wt_het,het_het_het
 ID-002,Line-ABC,15/12/2025,ID-F1,ID-M1,End of experiment,3,Mut-A,Mut-B,Mut-C,het_wt_hom,wt_wt_het,het_het_het
 ID-003,Line-ABC,02/01/2025,ID-F1,ID-M1,End of experiment,3,Mut-A,Mut-B,Mut-C,het_wt_hom,wt_wt_het,het_het_het
@@ -27,4 +27,4 @@ ID-025,Line-BCD,01/12/2025,ID-F11,ID-M11,End of experiment,3,Mut-B,Mut-C,Mut-D,w
 ID-026,Line-BCD,18/12/2025,ID-F12,ID-M12,End of experiment,3,Mut-B,Mut-C,Mut-D,wt_het_het,het_wt_het,wt_het_wt
 ID-027,Line-BCD,01/12/2025,ID-F13,ID-M13,End of experiment,3,Mut-B,Mut-C,Mut-D,wt_het_het,wt_het_wt,het_wt_het
 ID-028,Line-CDE,03/08/2025,ID-F14,ID-M14,End of experiment,3,Mut-C,Mut-D,Mut-E,het_het_hom,het_hom_hom,hom_het_hom
-ID-029,Line-CDE,03/08/2025,ID-F14,ID-M14,End of experiment,3,Mut-C,Mut-D,Mut-E,het_het_hom,het_hom_hom,hom_het_hom
+ID-029,Line-CDE,03/08/2025,ID-F14,ID-M14,End of experiment,3,Mut-C,Mut-D,Mut-E,het_het_hom,het_hom_hom,hom_het_hom

standardised-data-forbidden-genotypes.csv

@@ -1,4 +1,4 @@
-ID_offspring,line_name,date_of_birth,ID_father,ID_mother,sacrifice_reason,n_mutations,mutation_1,mutation_2,genotype_offspring,genotype_father,genotype_mother
+ID_offspring,line_name,date_of_birth,ID_father_1,ID_mother_1,sacrifice_reason,n_mutations,mutation_1,mutation_2,genotype_offspring,genotype_father,genotype_mother
 ID-001,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,2,Mut-A,Mut-B,het_hom,hom_het,wt_hom
 ID-006,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,2,Mut-A,Mut-B,het_hom,hom_het,wt_hom
 ID-007,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,2,Mut-A,Mut-B,het_hom,hom_het,wt_hom

standardised-data-forbidden-parents.csv

@@ -0,0 +1,2 @@
+ID_offspring,line_name,date_of_birth,ID_father_1,ID_father_2,ID_mother_1,ID_mother_2,sacrifice_reason,n_mutations,mutations,genotype_offspring,genotype_father,genotype_mother
+ID-006,Line-A,15/12/2025,ID-F1,ID-F2,ID-M1,ID-M2,End of experiment,1,Mut-A,hom,hom,het

standardised-data-forbidden-schemes.csv

@@ -1,4 +1,4 @@
-ID_offspring,line_name,date_of_birth,ID_father,ID_mother,sacrifice_reason,n_mutations,mutation_1,mutation_2,genotype_offspring,genotype_father,genotype_mother
+ID_offspring,line_name,date_of_birth,ID_father_1,ID_mother_1,sacrifice_reason,n_mutations,mutation_1,mutation_2,genotype_offspring,genotype_father,genotype_mother
 ID-001,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,2,Mut-A,Mut-B,hom_hom,het_hom,hom_het
 ID-002,Line-AB,15/12/2025,ID-F1,ID-M1,End of experiment,2,Mut-A,Mut-B,hom_hom,het_hom,hom_het
 ID-003,Line-AB,02/01/2025,ID-F1,ID-M1,End of experiment,2,Mut-A,Mut-B,het_hom,het_hom,hom_het

standardised-data-multiple-parents-1-mutation.csv

@@ -0,0 +1,7 @@
+ID_offspring,line_name,date_of_birth,ID_father_1,ID_father_2,ID_mother_1,ID_mother_2,sacrifice_reason,n_mutations,mutations,genotype_offspring,genotype_father,genotype_mother
+ID-001,Line-A,15/12/2025,ID-F1,ID-F2,ID-M1,ID-M2,End of experiment,1,Mut-A,hom,hom,het
+ID-002,Line-A,15/12/2025,ID-F1,ID-F2,ID-M1,ID-M2,End of experiment,1,Mut-A,het,het,hom
+ID-003,Line-A,02/01/2026,ID-F3,,ID-M3,ID-M4,End of experiment,1,Mut-A,het,hom,het
+ID-006,Line-A,15/02/2026,ID-F5,ID-F6,ID-M5,ID-M6,End of experiment,1,Mut-A,wt,wt,wt
+ID-007,Line-A,15/02/2026,ID-F5,ID-F6,ID-M5,ID-M6,End of experiment,1,Mut-A,het,het,wt
+ID-010,Line-A,15/03/2026,ID-F7,,ID-M5,ID-M8,End of experiment,1,Mut-A,hom,hom,hom

standardised-data-multiple-parents-2-mutations.csv

@@ -0,0 +1,6 @@
+ID_offspring,line_name,date_of_birth,ID_father_1,ID_father_2,ID_mother_1,ID_mother_2,sacrifice_reason,n_mutations,mutations,genotype_offspring,genotype_father,genotype_mother
+ID-001,Line-AB,15/12/2025,ID-F1,ID-F2,ID-M1,ID-M2,End of experiment,2,Mut-A_Mut-B,het_het,wt_het,het_wt
+ID-002,Line-AB,15/12/2025,ID-F1,ID-F2,ID-M1,ID-M2,End of experiment,2,Mut-A_Mut-B,hom_het,hom_wt,hom_het
+ID-004,Line-AB,02/01/2026,ID-F3,ID-F4,ID-M3,,End of experiment,2,Mut-A_Mut-B,het_het,hom_wt,het_het
+ID-007,Line-AB,15/02/2026,ID-F5,ID-F6,ID-M5,ID-M6,End of experiment,2,Mut-A_Mut-B,het_wt,het_wt,wt_wt
+ID-010,Line-AB,15/03/2026,ID-F7,,ID-M5,ID-M8,End of experiment,2,Mut-A_Mut-B,het_wt,het_het,het_wt

standardised-data-multiple-parents-3-mutations.csv

@@ -0,0 +1,7 @@
+ID_offspring,line_name,date_of_birth,ID_father_1,ID_father_2,ID_mother_1,ID_mother_2,sacrifice_reason,n_mutations,mutations,genotype_offspring,genotype_father,genotype_mother
+ID-001,Line-ABC,15/12/2025,ID-F1,ID-F2,ID-M1,ID-M2,End of experiment,3,Mut-A_Mut-B_Mut-C,wt_wt_hom,wt_wt_het,het_het_het
+ID-002,Line-ABC,15/12/2025,ID-F1,ID-F2,ID-M1,ID-M2,End of experiment,3,Mut-A_Mut-B_Mut-C,hom_wt_wt,het_het_het,hom_wt_het
+ID-003,Line-ABC,02/01/2026,ID-F3,,ID-M3,ID-M4,End of experiment,3,Mut-A_Mut-B_Mut-C,het_het_het,het_het_het,wt_het_het
+ID-004,Line-ABC,02/01/2026,ID-F3,,ID-M3,ID-M4,End of experiment,3,Mut-A_Mut-B_Mut-C,het_hom_het,het_hom_wt,wt_het_hom
+ID-007,Line-ABC,15/02/2026,ID-F5,ID-F6,ID-M5,ID-M6,End of experiment,3,Mut-A_Mut-B_Mut-C,het_wt_wt,het_wt_wt,wt_wt_wt
+ID-010,Line-ABC,15/03/2026,ID-F7,,ID-M5,ID-M8,End of experiment,3,Mut-A_Mut-B_Mut-C,het_wt_hom,het_wt_hom,wt_wt_hom