m_qtlmap_haplotype_external

[ Top ] [ Modules ]

NAME

    m_qtlmap_haplotype_external

DESCRIPTION

NOTES

SEE ALSO

haplotype_external

[ Top ] [ m_qtlmap_haplotype_external ] [ Subroutines ]

NAME

   haplotype_V1

DESCRIPTION

   Use the haplotype/phases for the F1 (sire and dam) given by the user (read order) [this information has been generated by an other tools than qtlmap]
   for each marker A B => A allele from the first chromosome (sire segment), B allele from the second chromosome

NOTES

  fill arrays : pdd,ngenom,ngend,ndesc,probg,phasp,phasm,genotyp,genotypm

SOURCE

 44     subroutine haplotype_external
 45       integer :: c,jm,kd,valnpo(nchr),i,ip,il
 46 
 47 
 48       allocate ( ngend(nchr,nm+1) )
 49       allocate ( probg(nchr,nm) )
 50       allocate ( ndesc(nchr,nd) )
 51       allocate ( genotypm(nchr,maxval(nmk),nm,2) )
 52       allocate ( ngenom(nchr,nm+1) )
 53       allocate ( phasp(nchr,np) )
 54       allocate ( phasm(nchr,nm) )
 55       allocate ( genotyp(nchr,maxval(nmk),(size(numero)),2) )
 56 
 57       ! structure de m_haplotype_V2
 58       allocate (ptfin(nchr,maxval(nmk),nd,4))
 59       allocate (prot(nchr,maxval(nmk),nd,4))
 60 
 61       call gammapf(prot)
 62 
 63       do c=1,nchr
 64        ngenom(c,1)=0
 65        do jm=1,nm
 66         probg(c,jm)=1.d0
 67         ngenom(c,jm+1)=ngenom(c,jm)+1
 68         ngend(c,jm)=ndm(jm)
 69         ngend(c,jm+1)=ndm(jm+1)
 70         do kd=ndm(jm)+1,ndm(jm+1)
 71           ndesc(c,kd)=kd
 72           do il=1,nmk(c)
 73             ptfin(c,il,kd,:)=prot(c,il,kd,:)
 74           end do
 75         end do
 76 
 77         if(correm(jm) /= 9999) then
 78           do il=1,nmk(c)
 79            genotypm(c,il,jm,1)=pheno(c,il,correm(jm),1)
 80            genotypm(c,il,jm,2)=pheno(c,il,correm(jm),2)
 81           end do !il
 82           phasm(c,jm)=.true.
 83         end if
 84        end do !jm
 85 
 86        do ip=1,np
 87         if(correp(ip) /= 9999) then
 88          do i=1,nmk(c)
 89             genotyp(c,i,correp(ip),1)=pheno(c,i,correp(ip),1)
 90             genotyp(c,i,correp(ip),2)=pheno(c,i,correp(ip),2)
 91          end do !i
 92          phasp(c,ip)=.true.
 93         end if
 94        end do !ip
 95 
 96       end do !c
 97 
 98       call setting_alloc_pdd()
 99       call pded_v5_optim()
100       call check_recombination_sire
101 
102       deallocate (ptfin)
103       deallocate (prot)
104 
105 
106 
107 
108     end subroutine haplotype_external