TABLE OF CONTENTS
- qtlmap
- toCarthagene
- ANALYSE
- m_qtlmap_analyse
- analyse
- analyse_cuda
- get_name_analyse
- get_type_data_analyse
- is_multitrait_analysis
- need_normalize_data
- opti_multitrait_DA
- opti_multitrait_modlin
- opti_multitraits
- opti_unitrait
- opti_unitrait_discret
- opti_unitrait_incidence
- opti_unitrait_incidence_cuda
- opti_unitrait_interaction
- opti_unitrait_modlin
- opti_unitrait_modlin_cox
- opti_unitrait_modlin_new
- quantile
- QUANTILE1
- W
- m_qtlmap_analyse_discret_unitrait
- funct_0qtl_discret_family
- funct_0qtl_discret_unitrait
- funct_1qtl_discret_family
- funct_1qtl_discret_unitrait
- opti_0qtl_discret_unitrait
- opti_1qtl_discret_unitrait
- set_solution_hypothesis0
- set_solution_hypothesis1
- test_lin
- m_qtlmap_analyse_gen
- cary
- carydf
- eff
- effdf
- effp
- estmum
- sig0
- somcd
- somcddf
- somy
- somydf
- xmu0m
- xmu0p
- courbe_lin_ldla
- end_analyse_gen
- get_eff_paternal_and_total
- init_analyse_gen
- optinit
- optinit_da
- scale_variables_dam
- set_ntnivmax
- m_qtlmap_analyse_lin_gen
- corniv
- covdir
- mcov
- meff
- mint
- nbco
- nbef
- nbfem
- nbniv
- nbnivest
- nivdir
- nteffmax
- ntlevm
- ntlevp
- ntnifix
- ntniv
- ntnivmax
- par0
- par1
- pb_haplo
- pm_ldla
- pmt
- pp_ldla
- ppt
- prbm
- prbp
- precis
- precis0
- precis1
- prop_haplo_info
- vecsol
- vecsol0
- vecsol1
- xinc
- xx
- xxx
- confusion
- contingence
- contingence_cox
- contingence_ldla
- end_analyse_lin_gen
- end_contingence
- init_analyse_lin_gen
- init_contingence
- precision
- prepinc
- set_filter_optim
- m_qtlmap_analyse_modlin
- current_chr
- current_ic
- f0
- fm0
- fm1
- fp0
- fp1
- sig1
- xmu1g
- xmu1m
- xmu1p
- end_analyse_modlin
- funct_0qtl_modlin
- funct_0qtl_modlin_family
- funct_1qtl_modlin
- funct_1qtl_modlin_family
- init_analyse_modlin
- opti_0qtl_modlin
- opti_1qtl_modlin
- set_solution_hypothesis0
- set_solution_hypothesis1
- test_lin
- m_qtlmap_analyse_modlin_cox
- current_chr
- current_ic
- f0
- fm0
- fm1
- fp0
- fp1
- Hy
- ntot
- posi_h1
- rangy
- sig1
- Ssy
- Sy
- xmu1m
- xmu1p
- yr
- yt
- calcul_rang
- end_analyse_modlin_cox
- funct_0qtl_modlin_cox
- funct_1qtl_modlin_cox
- init_analyse_modlin_cox
- opti_0qtl_modlin_cox
- opti_1qtl_modlin_cox
- set_solution_hypothesis0
- set_solution_hypothesis1
- test_lin_cox
- m_qtlmap_analyse_modlin_ldla
- f0
- fm0
- fm1
- fp0
- fp1
- sig1
- xmu1g
- xmu1m
- xmu1p
- end_analyse_modlin_ldla
- funct_0qtl_modlin_ldla_family
- funct_1qtl_modlin_ldla
- funct_1qtl_modlin_ldla_family
- init_analyse_modlin_ldla
- opti_0qtl_modlin_ldla
- opti_1qtl_modlin_ldla
- set_solution_hypothesis0
- set_solution_hypothesis1
- test_lin_ldla
- m_qtlmap_analyse_multitrait
- am
- ap
- carpm11
- carpp11
- carppdf11
- cary11
- carydf01
- corcd
- current_chr
- eff
- effdf
- effp
- estmum
- f01
- fm2
- fm21
- fp2
- fp21
- rhoi
- rhoi2
- rhoi2_1
- rhoi2_2
- sig01
- sig2
- sompm11
- sompmy11
- sompp11
- somppdf11
- somppm11
- somppy11
- somppydf11
- somy11
- somydf01
- somyy11
- somyydf01
- std
- xmoym
- xmoyp
- xmu01m
- xmu01p
- xmu2m
- xmu2p
- end_analyse_multitrait
- end_sub_1qtl
- funct_mcar_0qtl
- funct_mcar_0qtl_family
- funct_mcar_1qtl
- funct_mcar_1qtl_family
- init_analyse_multitrait
- init_sub_1qtl
- opti_mcar_0qtl
- opti_mcar_1qtl
- optinit_mcar
- set_solution_hypothesis0
- set_solution_hypothesis1
- m_qtlmap_analyse_multitrait_DA
- am
- ap
- carpm
- carpp
- carppdf
- current_chr
- f0
- f_1
- fm0
- fm1
- fm_1
- fp0
- fp1
- fp_1
- sig1
- sompm
- sompmy
- sompp
- somppdf
- somppm
- somppy
- somppydf
- std
- xmoym
- xmoyp
- xmu1m
- xmu1p
- end_analyse_DA_1QTL
- funct_0qtl
- funct_1qtl
- init_analyse_DA_1QTL
- opti_DA_0qtl
- opti_DA_1qtl
- perform_DA_1qtl
- set_solution_hypothesis1
- m_qtlmap_analyse_unitrait
- am
- am2
- ap
- ap2
- carpm
- carpm1
- carpm2
- carpp
- carpp1
- carpp2
- carppdf
- carppdf11
- carppdf12
- carppdf22
- current_chr
- current_chr2
- current_ic
- f0
- f_1
- fm0
- fm01
- fm1
- fm_1
- fm_2
- fp0
- fp01
- fp1
- fp_1
- fp_2
- sig1
- sompm
- sompm1
- sompm1m2
- sompm1y
- sompm2
- sompm2y
- sompmy
- sompp
- sompp1
- sompp1m1
- sompp1m2
- sompp1p2
- sompp1y
- sompp2
- sompp2m1
- sompp2m2
- sompp2y
- somppdf
- somppdf1
- somppdf2
- somppm
- somppy
- somppydf
- somppydf1
- somppydf2
- std
- std2
- xmoym
- xmoym2
- xmoyp
- xmoyp2
- xmu1m
- xmu1p
- end_analyse_unitrait_1QTL
- end_analyse_unitrait_2qtl
- end_sub_1qtl
- end_sub_2qtl
- funct_0qtl
- funct_0qtl_family
- funct_1car_2qtl
- funct_1car_2qtl_family
- funct_1qtl
- funct_1qtl_family
- init_analyse_unitrait_1QTL
- init_analyse_unitrait_2QTL
- init_sub_1qtl
- init_sub_2qtl
- opti_0qtl
- opti_1car_2qtl
- opti_1qtl
- print_incidence_solution
- set_solution_hypothesis0
- set_solution_hypothesis1
- set_solution_hypothesis2
- m_qtlmap_incidence
- DATASET_TYPE
- family_type
- INCIDENCE_GEN_STRUCT
- INCIDENCE_TYPE
- POSITION_LRT_INCIDENCE
- SireFamily_type
- INCIDENCE_INTERACTION
- INCIDENCE_TRAIT_COV
- INCIDENCE_TYPE_CLASSIC
- INCIDENCE_TYPE_LD
- INCIDENCE_TYPE_LDLA
- LINEAR_HETEROSCEDASTIC
- LINEAR_HOMOSCEDASTIC
- MAX_KD_PRINT
- OPTIM_HETEROSCEDASTIC
- likelyprob
- add_effcov
- add_general_mean
- add_haplotype_effect
- add_other_continue_traits_as_cov
- add_polygenic_effect
- add_qtleffect
- add_qtlinteraction
- build_incidence_matrix
- change_interaction_effect
- change_qtleffect
- confusion_between_qtl_and_effect
- confusion_type1
- copy_dataset
- copy_incidence_desc
- debug_write_incidence
- end_analyse_linear
- end_dataset
- end_incidence
- end_position
- estim_cholesky
- fill_nonull_elements
- gen_opti_nqtl
- gen_opti_nqtl_cuda
- get_correlations
- get_incidence_reduit
- get_precision
- getglobalprob
- getprob_lin
- getprobld_lin
- init_analyse_linear
- init_dataset_1car
- init_incidence
- init_position
- init_workstruct
- matmul_incidence
- model_XT_V_X
- model_XT_X
- opti_0qtl
- opti_0qtl_cuda
- opti_nqtl
- opti_nqtl_cuda
- pdd_at_position
- release_copy_incidence_desc
- release_ws
- set_corrxinc
- set_MR
- set_RHS
- set_RHS_V
- set_solution
- set_VInv
- test_nuisances
- m_qtlmap_incidence_linear
- model_lin_h0
- model_lin_hn
- modele_heteroscedastic
- modele_homoscedastic
- opti_0qtl_linear
- opti_2qtl_linear_interaction
- m_qtlmap_incidence_multi
- current_chr
- dataset
- estfem_multi
- estime_multi
- iam_multi
- my_listdesc
- my_xincreduitmul
- namest_multi
- ntnivmaxtotal
- add_effcov_multi
- add_general_mean_multi
- add_polygenic_effect_multi
- add_qtleffect_multi
- change_qtleffect_multi
- confusion_multi_type1
- end_incidence_multi
- gen_loop_opti_nqtl_multi
- gen_opti_nqtl_multi
- get_inv_residual_covariance_matrix
- get_inv_residual_covariance_matrix_cd
- get_inv_residual_covariance_matrix_LU
- get_inv_residual_covariance_matrix_LU_cd
- init_dataset_ncar
- init_incidence_multi
- init_startpoint
- likelihood_ncar_h0_family
- likelihood_ncar_h0_family_LU
- likelihood_ncar_h0_family_withcd
- likelihood_ncar_h0_LU
- likelihood_ncar_h0_LU_family_withcd
- likelihood_ncar_hn_family
- likelihood_ncar_hn_family_LU
- likelihood_ncar_hn_family_withcd
- likelihood_ncar_hn_LU
- likelihood_ncar_hn_LU_family_withcd
- model_optim_multi_family
- model_optim_multi_h0
- model_optim_multi_h0_LU
- model_optim_multi_hn
- model_optim_multi_hn_LU
- model_optim_multi_LU
- opti_0qtl_multi
- opti_nqtl_multi
- pdd_at_position_multi
- m_qtlmap_incidence_optim
- DATA
- m_qtlmap_constant
- AM_MAX
- AM_MIN
- ANALYSE_2QTL_INTERACTION
- ANALYSE_DEV_1
- ANALYSE_DEV_2
- ANALYSE_MULTIRAIT
- ANALYSE_MULTITRAIT_DA
- ANALYSE_MULTITRAIT_INCIDENCE
- ANALYSE_MULTITRAIT_INCIDENCE_LU
- ANALYSE_TRAIT_COV_CONTINGENCE
- ANALYSE_UNITRAIT
- ANALYSE_UNITRAIT_CONTINGENCE
- ANALYSE_UNITRAIT_LA
- ANALYSE_UNITRAIT_LD
- ANALYSE_UNITRAIT_LDJH
- ANALYSE_UNITRAIT_LDLA
- ANALYSE_UNITRAIT_LDLA_CROIS
- ANALYSE_UNITRAIT_LINEAR_LA_HETERO
- ANALYSE_UNITRAIT_LINEAR_LA_HOMO
- ANALYSE_UNITRAIT_LINEAR_LD_HETERO
- ANALYSE_UNITRAIT_LINEAR_LD_HOMO
- ANALYSE_UNITRAIT_LINEAR_LDLA_HETERO
- ANALYSE_UNITRAIT_LINEAR_LDLA_HOMO
- ANALYSE_UNITRAIT_MODLIN
- ANALYSE_UNITRAIT_MODLIN_COX
- AP_MAX
- AP_MIN
- BC_KEYWORD
- COMMON_ANALYSE
- DEFAULT_PARAM_MAX
- DEFAULT_PARAM_MIN
- DP
- EPS_EM
- F2_KEYWORD
- FMT_INT
- FMT_INT_LONG
- FMT_MAX_BUFFER
- FMT_REAL
- INIFINY_REAL_VALUE
- INT_NOT_DEFINED
- ITER_EM_MAX
- KIND_PHENO
- LABEL_GENEALOGY
- LABEL_MARKERS
- LABEL_NAME_TRAIT
- LABEL_QTL
- LABEL_SIMULTRAITS
- LABEL_TRAITS
- LEN_BUFFER_LINE
- LEN_BUFFER_WORD
- LEN_DEF
- LEN_L
- LEN_LINE
- LEN_S
- LEN_W
- LENGTH_MAX_FILE
- MAX_FILES_INPUT
- MAXNB_KEY_DEV_GEN
- OPT_SIB_FS
- OPT_SIB_HS
- OUTBRED_KEYWORD
- REAL_NOT_DEFINED
- SIG_MAX
- SIG_MIN
- SIMULATION
- STRING_NOT_DEFINED
- TRANSCIPTOME_ANALYSE
- TYPE_DATA_CONTINUE
- TYPE_DATA_COX
- VAL_MAX_INDEX_PHENO
- VAL_MIN_INDEX_PHENO
- XMU_MAX
- XMU_MIN
- m_qtlmap_data
- absi
- alleles
- animal
- BASE_STEP
- bete
- carac
- cd
- ch
- chromo
- corperf
- corred
- corregm
- corregp
- correm
- correp
- correr
- covar
- EPS_LINEAR_HETEROSCEDASTIC
- estfem
- estime
- femelle
- geneaFileDefined
- genotypeFileDefined
- gmere
- gpere
- h2
- iam
- in_carte
- in_genea
- in_param_ef
- in_parsim
- in_perfs
- in_race
- in_typage
- indicemod
- listelev
- listModelTrait
- mapFileDefined
- mark
- MAX_LINEAR_ITERATION
- mere
- modele
- nall
- namecov
- namefix
- namest
- natureY
- nb_value_pheno
- ncar
- ncarcat
- nchr
- ncov
- nd
- ndelta
- ndm
- NDMIN
- nfem
- nfix
- ngm
- ngmgp
- ngp
- nivx
- nlev
- nm
- NMANQUE
- nmes
- nmk
- nmod
- nmp
- nmumest
- np
- nrgm
- numero
- opt_sib
- optim_H_PRECISION
- optim_maxeval
- optim_maxtime
- optim_tolf
- optim_tolg
- optim_tolx
- PAS
- pc_all
- pere
- pheno
- PHPSEUIL
- posi
- posif
- posim
- presentc
- presentg
- PROB_PHASE_DESC
- PROB_SEUIL_RECOMB
- prop
- PRSEUIL
- PSEUILHWE
- raceFileDefined
- rep_reprom
- rep_reprop
- repfem
- repmere
- reppere
- repro
- reprom
- reprop
- rf
- RhoG
- RhoP
- rm
- seuil
- SEUIL_CHO
- sigt
- simTyp
- simulGenea
- simulMap
- simulTraits
- tabDevKey
- THRES_CONFUSION
- traitsFileDefined
- value_pheno
- xmut
- y
- ycategorial
- ydiscretord
- m_qtlmap_haplotype_data
- comp_haplo_reduit
- count_haplo
- genotyp
- genotypm
- liste_haplo_reduit
- LONG_MIN_IBS
- longhap
- name_haplo
- name_haplo_complet
- name_haplo_reduit
- nb_gam
- nb_gam_desc
- nb_gam_mere
- nb_gam_pere
- nb_haplo
- nb_haplo_complet
- NB_HAPLO_PRIOR
- nb_max_haplo
- ndesc
- ngend
- ngenom
- num_haplo_desc
- num_haplo_mere
- num_haplo_pere
- pb_haplo_desc
- pb_haplo_reduit
- pdd
- phasm
- phasp
- prob_gam
- prob_gam_mere
- prob_gam_pere
- PROB_HAPLO_MIN
- prob_seuil_gam
- probg
- reconstructed
- shared_haplo
- tab_IBS
- tab_shared_haplo
- QTLMAP_TYPES
- INPUT
- m_qtlmap_genealogy
- calculCd
- genea_list
- genea_niv
- genealogy_outbred_gen
- rac
- CREATE_STRUCT_GRAND_PARENT
- CREATE_STRUCT_PARENT
- log_debug_genea
- read_genealogy
- sim_genea
- sim_genea_F2_BC
- sim_genea_outbread
- write_genea
- m_qtlmap_genotype
- unit_genotype
- index_position_marker
- nmarker_in_genotype_file
- allocate_vector_
- check_HWE
- check_marker_name
- check_typage
- confbin
- internal_read_file
- read_genotype
- recup
- set_allele_info_vector
- set_corresponding_vector
- set_estfem
- sim_typ
- write_typ
- m_qtlmap_map
- MAX_SIZE_MAP
- mark0
- mselec
- posi0
- posif0
- posim0
- check_map
- chromo_is_select
- INIT_INTERNAL_MAP_STRUCTURE
- read_map
- sim_carte
- write_map
- m_qtlmap_parameter_file
- K_CHOLESKY
- K_CHROM
- K_COEFFDA
- K_FREQALL
- K_GENEA
- K_GENOTYPE
- K_GRID2QTL
- K_HAPLOTYPES
- K_KEY_DEV_GEN
- K_LINEAR_CONV
- K_LONG_MIN_IBS
- K_LONGHAP
- K_LRTDAM
- K_LRTSIRE
- K_MAP
- K_MATEFF
- K_MAX_LINEAR_ITERATION
- K_MINDAMPHASEPROB
- K_MINSIREPHASEPROB
- K_MODEL
- K_NB_HAPLO_PRIOR
- K_NDMIN
- K_OPTIM_H_PREC
- K_OPTIM_MAXEVAL
- K_OPTIM_MAXTIME
- K_OPTIM_TOLF
- K_OPTIM_TOLG
- K_OPTIM_TOLX
- K_OUTPUT
- K_OUTSIM
- K_PARAMSIM
- K_PATEFF
- K_PDECPLE
- K_PDED
- K_PHASES
- K_PHASES_OFFSPRING
- K_PHASES_OFFSPRING_MARK_END
- K_PHASES_OFFSPRING_MARK_START
- K_PROB_HAPLO_MIN
- K_PROB_SEUIL_RECOMB
- K_PSEUILHWE
- K_RACE
- K_STEP
- K_SUMM
- K_THRES_CONFUSION
- K_TRAITS
- K_UNKNOWN_GENO
- NUMBER_ALL_KEYS
- NUMBER_AUTO_KEYS
- NUMBER_OPT_KEYS
- all_key
- default_values
- index_key
- keys
- values
- end_analyse_parameterfile
- get_key_value
- get_summary_panalyse
- help_panalyse
- initialize_dev_generic_keys
- initialize_qtlmap_context
- initialize_tocartha_context
- key_exist
- key_exist_file
- read_analyse_file
- set_haplotype_offspring_context
- m_qtlmap_simulation
- ios_simul_file
- current_line
- init_genotype_simul
- init_permutation
- init_simul_genealogy
- init_simul_marker
- init_traits_simul
- read_attributes_discrete_trait
- read_correlation_matrix
- read_qtl_effect_on_trait
- read_simulation_file
- set_simulation_genealogy
- set_simulation_marker
- set_simulation_qtl
- set_simulation_simultraits
- set_simulation_traits
- set_soglia
- m_qtlmap_traits
- ALL_LABEL_MODEL
- MAX_QTL
- NB_DES_MIN
- unit_mod
- unit_perf
- carac_t
- cdt
- cov
- h2_t
- int_qtl
- int_qtl_t
- natureY_t
- nb_qtl_def
- ndelt
- niv
- nuis
- nuis_t
- RhoG_t
- RhoP_t
- valeur
- check_cd
- check_traits_and_fathers
- fixe_structure_model
- init_model_struct
- init_random
- initialise_struct_internal
- log_infoqtldefinedbyuser
- manage_data
- manage_simulator_traits
- normal
- normalize_data
- read_model
- read_perf_by_column
- read_perf_by_line
- read_traits
- set_count_discrete
- set_estime
- set_proportion_discrete
- sim_perf_shuffling
- sim_perf_tirage
- sim_QTL
- sim_transform_discret
- write_perf
- LOG
- OUTPUT
- m_qtlmap_format_carthagene
- m_qtlmap_output_handler
- create_grid_file_2QTL
- end_output_handler
- init_output_handler
- log_descriptif_genealogy
- log_descriptif_traits
- log_marker_description
- log_simulation_message
- print_allelic_origin
- print_coeff_linear_combination
- print_coeff_linear_combination_max
- print_confusion
- print_courbe_LRT
- print_dam_phase
- print_end_multitraits
- print_end_unitrait
- print_freqall
- print_incidence_solution_risk_factor
- print_LRT
- print_LRT_2QTL
- print_lrt_solution
- print_maximum_LRT
- print_offspring_phase
- print_pat_mat_effect_2QTL
- print_paternal_maternal_effect
- print_pded
- print_residual_correlation
- print_resume_simulation
- print_resume_simulation_2
- print_sire_phase
- print_start_multitrait_DA
- print_start_multitraits
- print_start_unitrait
- print_summary_analyse
- print_summary_panalyse
- print_test_nuisances
- print_transcriptome
- print_transcriptome_H0
- print_transcriptome_Struct_famille
- set_file_output
- set_xml_output
- write_simulation_file
- m_qtlmap_output_xml
- m_qtlmap_output_xml/print_pded_xml
- TOOLS
- m_qtlmap_cd
- add_animal_genea
- calcul_corcd
- calcul_y_cd
- extend
- extendListCorrAnim
- extendListNa
- extendListTrio
- get_listProgenies
- init_perf_animal
- m_qtlmap_isymmax2sat
- m_qtlmap_math
- MATH_QTLMAP_F01ADF
- MATH_QTLMAP_F03ABF
- MATH_QTLMAP_G01AAF
- MATH_QTLMAP_G01EAF
- MATH_QTLMAP_G01EBF
- MATH_QTLMAP_G01ECF
- MATH_QTLMAP_G01EEF
- MATH_QTLMAP_G01FAF
- MATH_QTLMAP_G03ACF
- MATH_QTLMAP_G05EHF
- MATH_QTLMAP_INFO
- MATH_QTLMAP_INVDETMAT
- MATH_QTLMAP_INVDETMATSYM
- MATH_QTLMAP_LOWERTAIL_BETA
- MATH_QTLMAP_M01CAF
- MATH_QTLMAP_M01DAF
- MATH_QTLMAP_S15ADF
- MATH_QTLMAP_S15AEF
- m_qtlmap_optimization
- LIBNAG_AVAILABLE
- OPT_CLASSIC
- OPT_FAM
- OPT_FAM_MULTI
- OPT_FAM_SIRE
- OPTI_LAST
- OPTI_LBFGS
- OPTI_NAG
- determ
- filter_vci
- inv_vci
- NB_OPTI_NLOPT
- opti_user
- opti_user_fam
- get_gradient
- get_gradient_optim_fam
- get_gradient_optim_fam_multi
- get_gradient_optim_fam_sire
- get_inv_residual_covariance_matrix
- get_value
- get_value_optim_fam
- get_value_optim_fam_multi
- get_value_optim_fam_sire
- likelihood_empty
- minimizing_e04jyf
- minimizing_funct
- minimizing_funct_family
- minimizing_funct_family_multi
- minimizing_funct_family_sire
- minimizing_lbfgs
- minimizing_nlopt
- name_optim
- set_optimization
- m_qtlmap_solve_linear
- m_qtlmap_tools
- check_allocate
- clean_lrt_solution
- copy
- copy_description_type
- dget_str
- EXTRACT
- fget_str
- file_exist
- GET
- get_dx
- get_ilong
- get_ind_pheno
- get_int
- get_int_char
- get_long_step_morgan
- get_maxnbgenotypedam
- get_maxnpo
- get_npo
- get_pheno
- get_pos
- get_real
- get_real_char
- iget_str
- init_pheno
- new
- new_lrt_solution
- next_word
- next_word_char
- parse_real_array
- release
- release_data
- release_description_type
- release_incidence_solution
- release_lrt_solution
- release_model_trait
- REMOVE
- set_absi
- set_base_and_step
- set_pheno
- stop_application
- stop_on_error
- str
- xaldane
- xosambi
- m_qtlmap_cli
- LEN_OPT
- MARG_HELP
- NQTL_DEFAULT
- NSIM_DEFAULT
- OPT_CALCUL
- OPT_CENSORED_CALCUL
- OPT_DEBUG
- OPT_DEBUG_SHORT
- OPT_EQTL
- OPT_ESTIME_THRESHOLDS
- OPT_ESTIME_THRESHOLDS_SHORT
- OPT_HAPLOTYPE
- OPT_HDAM
- OPT_HELP
- OPT_HELP_PANALYSE
- OPT_HELP_PARAMSIM
- OPT_NOPOLY
- OPT_NSIM
- OPT_OPTIM
- OPT_PERMUT
- OPT_PRINT_CLASSIC
- OPT_QTL
- OPT_QUIET
- OPT_QUIET_SHORT
- OPT_SIBF
- OPT_SIM
- OPT_SNP
- OPT_VERBOSE
- OPT_VERBOSE_SHORT
- OPT_XML
- OPTIM_DEFAULT
- SIB_DEFAULT
- cli_get_analyse
- cli_get_family
- cli_get_haplotype
- cli_get_nqtl
- cli_get_nsim
- cli_get_optimization
- cli_get_parameters_file
- cli_is_calcul_cd
- cli_is_debug
- cli_is_estimate_thresholds
- cli_is_hdam
- cli_is_help
- cli_is_help_panalyse
- cli_is_help_paramsim
- cli_is_nopoly
- cli_is_nsim
- cli_is_permute
- cli_is_print_all
- cli_is_quiet
- cli_is_simulation
- cli_is_transcriptomic_data
- cli_is_verbose
- cli_is_xmloutput
- cli_print_help
- cli_print_qtlmap_version
- get_arg
- get_binary_name
- get_key_value
- get_nb_arg
- key_exist
- to_integer
- m_qtlmap_haplotype
- VERSION_HAPLOTYPE_PARENTAL_EXTERNAL
- VERSION_HAPLOTYPE_SNP
- VERSION_HAPLOTYPE_SNP_PRINT
- VERSION_HAPLOTYPE_SYMMAX2SAT_SNP
- VERSION_HAPLOTYPE_V1
- VERSION_HAPLOTYPE_V2
- VERSION_HAPLOTYPE_V3
- get_pdd_at_mark
- haplotype
- haplotype_offspring
- test_print_haplotype
- m_qtlmap_haplotype_external
- m_qtlmap_haplotype_ldla
- comp_haplo
- count_haplo_complet
- gamete
- haplo
- haplo_complet
- loc_haplo
- nb_haplo_possible
- pb_haplo_complet
- race_h
- race_haplo_complet
- tab_haplo_complet
- bilan_shared_haplo
- check_change_maker_windows
- free_internal_struct_ldla
- global_gamete
- liste_gamete
- liste_haplo
- liste_haplo_complet
- liste_shared_haplo
- local_gamete
- point_gamete
- proba_haplo_complet
- set_allocation
- set_haplo_final
- set_haplo_for_ldla
- set_tab_ibs
- sort_haplo
- tri_haplo_complet
- m_qtlmap_haplotype_V1
- m_qtlmap_haplotype_V2
- MAX_CAS_ALLOC
- MAX_MARKER
- ordre
- ordref
- ordrem
- ordrep
- prot
- ptfin
- ancetre
- calcul_phases_symmax2sat_dam
- calcul_phases_symmax2sat_sire
- check_recombination_sire
- free_internal_struct
- haplotype_SNP
- haplotype_SYMMAX2SAT_SNP
- haplotype_V2
- haplotype_V3
- pded
- pded_v5
- pded_v5_kd
- pded_v5_optim
- pdegm
- pdegm_snp
- pdegp
- pdegp_snp
- probin
- set_allocation
- set_phasm
- set_phasp
- setting_alloc_pdd
- m_qtlmap_phase_offspring