m_qtlmap_haplotype
NAME
m_qtlmap_haplotype
DESCRIPTION
NOTES
SEE ALSO
VERSION_HAPLOTYPE_PARENTAL_EXTERNAL
[ Top ] [ m_qtlmap_haplotype ] [ Constants ]
NAME
VERSION_HAPLOTYPE_PARENTAL_EXTERNAL
DESCRIPTION
Constant for external calcultion of phases
NOTES
SOURCE
106 integer, public, parameter :: VERSION_HAPLOTYPE_PARENTAL_EXTERNAL = 7
VERSION_HAPLOTYPE_SNP
[ Top ] [ m_qtlmap_haplotype ] [ Constants ]
NAME
VERSION_HAPLOTYPE_SNP
DESCRIPTION
Constant for the 4th version of the haplotypes routines
NOTES
Elsen JM. A fast algorithm for estimating transmission probabilities in QTL detection designs with dense maps.
SOURCE
72 integer, public, parameter :: VERSION_HAPLOTYPE_SNP = 4 !
VERSION_HAPLOTYPE_SNP_PRINT
[ Top ] [ m_qtlmap_haplotype ] [ Constants ]
NAME
VERSION_HAPLOTYPE_SNP_PRINT
DESCRIPTION
Constant for the 4th version of the haplotypes routines
NOTES
Elsen JM. A fast algorithm for estimating transmission probabilities in QTL detection designs with dense maps. CMO added the routine haplotype to print the offspring haplotypes
SOURCE
95 integer, public, parameter :: VERSION_HAPLOTYPE_SNP_PRINT = 6 !
VERSION_HAPLOTYPE_SYMMAX2SAT_SNP
[ Top ] [ m_qtlmap_haplotype ] [ Constants ]
NAME
VERSION_HAPLOTYPE_SNP
DESCRIPTION
Constant for the 5th version of the haplotypes routines
NOTES
Phases are computed by Symmax2Sat Elsen JM. A fast algorithm for estimating transmission probabilities in QTL detection designs with dense maps.
SOURCE
84 integer, public, parameter :: VERSION_HAPLOTYPE_SYMMAX2SAT_SNP = 5 !
VERSION_HAPLOTYPE_V1
[ Top ] [ m_qtlmap_haplotype ] [ Constants ]
NAME
VERSION_HAPLOTYPE_V1
DESCRIPTION
Constant for the first version of the haplotypes routines
NOTES
SOURCE
39 integer, public, parameter :: VERSION_HAPLOTYPE_V1 = 1 ! Original version
VERSION_HAPLOTYPE_V2
[ Top ] [ m_qtlmap_haplotype ] [ Constants ]
NAME
VERSION_HAPLOTYPE_V2
DESCRIPTION
Constant for the second version of the haplotypes routines
NOTES
SOURCE
50 integer, public, parameter :: VERSION_HAPLOTYPE_V2 = 2 !
VERSION_HAPLOTYPE_V3
[ Top ] [ m_qtlmap_haplotype ] [ Constants ]
NAME
VERSION_HAPLOTYPE_V3
DESCRIPTION
Constant for the third version of the haplotypes routines
NOTES
SOURCE
61 integer, public, parameter :: VERSION_HAPLOTYPE_V3 = 3 !
get_pdd_at_mark
[ Top ] [ m_qtlmap_haplotype ] [ Subroutines ]
NAME
get_pdd_at_mark
DESCRIPTION
Get the index position of the array pdd (prob of transmission) at the position : marker lk on the chromosome ch.
INPUTS
ch : index chromosome lk : index marker
OUTPUTS
pos : index position
SOURCE
202 subroutine get_pdd_at_mark(ch,lk,pos) 203 integer , intent(in) :: ch 204 integer , intent(in) :: lk 205 integer , intent(out) :: pos 206 207 real(kind=dp) ,parameter :: epsil = 0.001 208 209 integer :: istart,iend 210 211 212 213 end subroutine get_pdd_at_mark
haplotype
[ Top ] [ m_qtlmap_haplotype ] [ Subroutines ]
NAME
m_qtlmap_haplotype
DESCRIPTION
Apply the algorithm identify by opt_version
- Initialisation of the following structures : pdd, genotyp, genotypm, ngenom, ngend, ndesc, probg, phasp, phasm
INPUTS
opt_version : the version of the haplotype to used
SOURCE
122 subroutine haplotype(opt_version) 123 integer , intent(in) :: opt_version 124 125 !free structure if allocated 126 if ( allocated(pdd) ) deallocate( pdd ) 127 if ( allocated(ngend) ) deallocate( ngend ) 128 if ( allocated(ndesc) ) deallocate( ndesc ) 129 if ( allocated(probg) ) deallocate( probg ) 130 if ( allocated(genotyp) ) deallocate( genotyp ) 131 if ( allocated(genotypm) ) deallocate( genotypm ) 132 if ( allocated(ngenom) ) deallocate( ngenom ) 133 if ( allocated(phasp) ) deallocate( phasp ) 134 if ( allocated(phasm) ) deallocate( phasm ) 135 136 select case (opt_version) 137 138 case (VERSION_HAPLOTYPE_V1) 139 call log_mess('Computation of transmission probabilities V1',INFO_DEF) 140 call haplotype_V1() 141 142 case (VERSION_HAPLOTYPE_V2) 143 call log_mess('Computation of transmission probabilities V2',INFO_DEF) 144 call haplotype_V2() 145 146 case (VERSION_HAPLOTYPE_V3) 147 call log_mess('Computation of transmission probabilities V3',INFO_DEF) 148 call haplotype_V3() 149 150 case (VERSION_HAPLOTYPE_SNP) 151 call log_mess('Computation of transmission probabilities SNP',INFO_DEF) 152 call haplotype_SNP() 153 154 case (VERSION_HAPLOTYPE_SYMMAX2SAT_SNP) 155 call log_mess('Phases SYMMAX2SAT + Computation of transmission probabilities SNP',INFO_DEF) 156 call haplotype_SYMMAX2SAT_SNP() 157 158 case (VERSION_HAPLOTYPE_PARENTAL_EXTERNAL) 159 call log_mess('Parents phases are given by the user + Computation of transmission probabilities',INFO_DEF) 160 call haplotype_external() 161 162 163 case default 164 call stop_application('bad value of opt_version['//trim(str(opt_version))//'].') 165 end select 166 167 end subroutine haplotype
haplotype_offspring
[ Top ] [ m_qtlmap_haplotype ] [ Subroutines ]
NAME
haplotype_offspring
DESCRIPTION
Apply the algorithm identify by opt_haplotype_offspring
- Initialisation of the following structures : genotyp,reconstructed
INPUTS
opt_version : the version of the haplotype to used
SOURCE
179 subroutine haplotype_offspring(opt_version) 180 integer , intent(in) :: opt_version 181 182 !free structure if allocated 183 if ( allocated(reconstructed) ) deallocate( reconstructed ) 184 call haplotype_offspring_v1 185 186 187 end subroutine haplotype_offspring
test_print_haplotype
[ Top ] [ m_qtlmap_haplotype ] [ Subroutines ]
NAME
test_print_haplotype
DESCRIPTION
SOURCE
222 subroutine test_print_haplotype 223 224 ! real (kind=dp) ,dimension(:,:,:,:),allocatable :: prot 225 ! allocate (prot(nchr,maxval(nmk),nd,4),STAT=stat) 226 ! 227 ! call gammapf(prot) 228 ! 229 ! do ip=1,np 230 ! do jm=nmp(ip)+1,nmp(ip+1) 231 ! do geno=ngenom(jm)+1,ngenom(jm+1) 232 ! do kd=ngend(geno)+1,ngend(geno+1) 233 ! kkd=ndesc(kd) 234 ! !! animal s ALL_M1 ALL_M2 .... origine : 1/2 235 ! end do 236 ! end do 237 ! end do 238 ! end do 239 ! 240 ! deallocate (prot) 241 242 end subroutine test_print_haplotype