QeNb*$PS,xpTxT0_inbase2fill_haplologit_nr_haplologit_nrxadditiverecessivedominantem_haplo_di_haplotypes_genot2diplot_getindex_num2binh K Kbxbase2iiincolinbaseb7P ZQ[7Y=(f>Q[ Q_4LR&@'0h K Kbxbase2iiincolinbaseb7P ZQ[7Y=(f>Q[ Q_4LR&@'0@  LfyfLfsidfind1find2fhapxbvfs1vftmpvftmpv1fhapxbcp%datamat%sidpanel%subjects%hap_xb1%riskhapmat%rhapconsmat%scores%tmpmatiriskhapiKivarind_Linriskhapinriskhparmsinscoresinsubjiindiiijinumerikij3idenomid1effid1nuij1icoefij2ii1ii2strtorealpanelsetuppanelsubview(l7:7oQ(n7:77z)Q(r7:7z)Q(l7:7z)Q(t7:7z)Q(v7:7z)Q(y7:7z)(|7:7> 7(7;7>(7;7>7(7:*(7;*PO7:: P+7OP W Qf[,) Qh[,)7 P[PP[pwf [P[pwFP[ ]HF ]HF7E>F7P aP[pw> P[P[ NE>F7I P_P  $!!@!@F> P[ NE>F7I P_gO"O#O$PO7P%% P&%'' P[PP[%'pw f  [P[%'pw  %"& %] '] P[  7 "P zP[&P[%'pwP[  %]  '] 7 P_8% % (' )P([f %] '] P[  7 P(_%'' P)[f %] '] P[  7 P)_f&'P P[P[P["I$P_P  BP[P["I$P_""I77P)}7>)*Z&@@' Lriskhapxbybyhap1hap2numatMY_riskhapmatMY_rhapconsmatnriskhparmsML_k@  LfyfLfsidfind1find2fhapxbvfs1vftmpvftmpv1fhapxbcp%datamat%sidpanel%subjects%hap_xb1%riskhapmat%rhapconsmat%scores%tmpmatiriskhapiKivarind_Linriskhapinriskhparmsinscoresinsubjiindiiijinumerikij3idenomid1effid1nuij1icoefij2ii1ii2strtorealpanelsetuppanelsubview(l7:7oQ(n7:77z)Q(r7:7z)Q(l7:7z)Q(t7:7z)Q(v7:7z)Q(y7:7z)(|7:7> 7(7;7>(7;7>7(7:*(7;*PO7:: P+7OP W Qf[,) Qh[,)7 P[PP[pwf [P[pwFP[ ]HF ]HF7E>F7P aP[pw> P[P[ NE>F7I P_P  $!!@!@F> P[ NE>F7I P_gO"O#O$PO7P%% P&%'' P[PP[%'pw f  [P[%'pw  %"& %] '] P[  7 "P zP[&P[%'pwP[  %]  '] 7 P_8% % (' )P([f %] '] P[  7 P(_%'' P)[f %] '] P[  7 P)_f&'P P[P[P["I$P_P  BP[P["I$P_""I77P)}7>)*Z&@@' Lriskhapxbybyhap1hap2numatMY_riskhapmatMY_rhapconsmatnriskhparmsML_k  LfyfxbfLfsidfind1find2fhapxbvfs1vftmpvftmpv1fhapxbcp%datamat%sidpanel%subjects%hap_xb1%rhapvars%riskhapmat%rhapconsmat%scores%tmpmatiriskhapiKivarind_Livarind_g1inriskhapinriskhparmsin1inrhparmsmatinscoresinsubjiindiiijinumerik1ik2ikij3idenomid1xbid1effid1nuij1icoefij2ii1ii2strtorealpanelsetuppanelsubview(R7:7o(T7:7oQ(V7:77z)Q(Z7:77z)Q(]7:7z)Q(_7:7z)Q(R7:7z)Q(a7:7z)Q(c7:7z)Q(f7:7z)(i7:7> 7(l7;7>(q7;7>7(v7:2(z7:72(~7;2(7;2$PO7::P37 O!P""  <QL["4)QN["4)!7 !!P[PP[pwL## N!#[P#[pwF#'!P[ ]HF ]HF7  E>F7$P%P&P## KP#[pw > P#[P''  !&[ P%[!P[ NE>F7$I P%_%&'P#[P P%[!P[ NE>F7$I P%_E !&[ P%[!P[ NE>F7$I P%_&%#P ## #$((@(@F > P#[ NE>F7$I P#_#Q$!P[!P[7$O)O*O+O,PO7P-- P.-// !P[PP[-/pw L##  !#[P#[-/pw  #-). -] /] 7P!P[ 7  )*.  -]  /] 7 *P%P&P## 3P#[P'' P%[.!&[P#[-/pw  -]  /] 7 P%_%&'pP#[P P%[.P#[-/pw  -]  /] 7 P%_-P%[.!&[P#[-/pw  -]  /] 7 P%_&%#^- - 0/ 1P0[L -] /] 7P!P[ 7  P0_-// P1[L -] /] 7P!P[ 7  P1_L./P## P#[!P[7P#[)I$P#_#P ## P#[P#[)I$P#_#!$)I77P)!!P[!P[7*)I$7P)"7>)*ZR&@@'Lg1riskhapxbxrhvarsyxbbyhap1hap2numatMY_riskhapmatMY_rhapconsmatnriskhparmsnrhparmsML_kML_k1  LfyfxbfLfsidfind1find2fhapxbvfs1vftmpvftmpv1fhapxbcp%datamat%sidpanel%subjects%hap_xb1%rhapvars%riskhapmat%rhapconsmat%scores%tmpmatiriskhapiKivarind_Livarind_g1inriskhapinriskhparmsin1inrhparmsmatinscoresinsubjiindiiijinumerik1ik2ikij3idenomid1xbid1effid1nuij1icoefij2ii1ii2strtorealpanelsetuppanelsubview(R7:7o(T7:7oQ(V7:77z)Q(Z7:77z)Q(]7:7z)Q(_7:7z)Q(R7:7z)Q(a7:7z)Q(c7:7z)Q(f7:7z)(i7:7> 7(l7;7>(q7;7>7(v7:2(z7:72(~7;2(7;2$PO7::P37 O!P""  <QL["4)QN["4)!7 !!P[PP[pwL## N!#[P#[pwF#'!P[ ]HF ]HF7  E>F7$P%P&P## KP#[pw > P#[P''  !&[ P%[!P[ NE>F7$I P%_%&'P#[P P%[!P[ NE>F7$I P%_E !&[ P%[!P[ NE>F7$I P%_&%#P ## #$((@(@F > P#[ NE>F7$I P#_#Q$!P[!P[7$O)O*O+O,PO7P-- P.-// !P[PP[-/pw L##  !#[P#[-/pw  #-). -] /] 7P!P[ 7  )*.  -]  /] 7 *P%P&P## 3P#[P'' P%[.!&[P#[-/pw  -]  /] 7 P%_%&'pP#[P P%[.P#[-/pw  -]  /] 7 P%_-P%[.!&[P#[-/pw  -]  /] 7 P%_&%#^- - 0/ 1P0[L -] /] 7P!P[ 7  P0_-// P1[L -] /] 7P!P[ 7  P1_L./P## P#[!P[7P#[)I$P#_#P ## P#[P#[)I$P#_#!$)I77P)!!P[!P[7*)I$7P)"7>)*ZR&@@'Lg1riskhapxbxrhvarsyxbbyhap1hap2numatMY_riskhapmatMY_rhapconsmatnriskhparmsnrhparmsML_kML_k1% K K K@@FK% K K K@@FK% K K K@@>K% K K K@@>K% K K K@@;K% K K K@@;K  K L K K L L Lcpcpnextctmpvcpanelsum%matind%tmpm%index%subjectsiiijiKinsubjidenomillinobsinindexiiteritolii1ii2itmpipdifficutoffhhapfindfind1find2fple1panelsetuppanelsubviewmeanmaxpanelstatsrangestrtorealinbase Q(7:77o(7:7z)OOQ7  Q[ Q[:  P#7(7:( u(7:7>OCPD;71O K(7)(7)7)P71$:]O (7)(7)7)PPI7PO7O7 OQ( (7) ( (7)7O (7)7)OP  $)7QP[ Q[!P a ]!]]] [ _  [ _  Q[71 Q[IQ_ 7  %O7 $C"">?P"=> 7 &( (P$7)O P ) $)QP[]Q[]>  QP[Q[EH> 717 ( ;(7)(7O S(7)' PP((7:( y(7:)|OHA7a7O (7)((71 ( 7)7)HHA7a( P[7<)( PP[7<)( P[7<)( P[7<)(7<)( 7<)(7<) (P7<)%(O7<)H7>)7P(7(71F:7@)(H7>)( v*7Y=(> }71*ZR&@@h@I@{Gz? @@'varlisttouseeminit eminit(): specified haplotype frequencies must be between 0 and 1\n eminit(): the sum of specified frequencies exceed one\n\n{txt}. %g\n{txt}Iteration %g:{col 16}Sample log-likelihood = {res}%10.0g\nonlycutoffcutoff All estimated haplotype frequencies are less than tolerance %8.0ge(N)e(N_s)e(N_min)e(N_max)e(N_snp)e(ll)e(iter)e(converged)hap_e(index)0  K L K K L L Lcpcpnextctmpvcpanelsum%matind%tmpm%index%subjectsiiijiKinsubjidenomillinobsinindexiiteritolii1ii2itmpipdifficutoffhhapfindfind1find2fple1panelsetuppanelsubviewmeanmaxpanelstatsrangestrtorealinbase Q(7:77o(7:7z)OOQ7  Q[ Q[:  P#7(7:( u(7:7>OCPD;71O K(7)(7)7)P71$:]O (7)(7)7)PPI7PO7O7 OQ( (7) ( (7)7O (7)7)OP  $)7QP[ Q[!P a ]!]]] [ _  [ _  Q[71 Q[IQ_ 7  %O7 $C"">?P"=> 7 &( (P$7)O P ) $)QP[]Q[]>  QP[Q[EH> 717 ( ;(7)(7O S(7)' PP((7:( y(7:)|OHA7a7O (7)((71 ( 7)7)HHA7a( P[7<)( PP[7<)( P[7<)( P[7<)(7<)( 7<)(7<) (P7<)%(O7<)H7>)7P(7(71F:7@)(H7>)( v*7Y=(> }71*ZR&@@@h@I?zG{@ @'varlisttouseeminit eminit(): specified haplotype frequencies must be between 0 and 1\n eminit(): the sum of specified frequencies exceed one\n\n{txt}. %g\n{txt}Iteration %g:{col 16}Sample log-likelihood = {res}%10.0g\nonlycutoffcutoff All estimated haplotype frequencies are less than tolerance %8.0ge(N)e(N_s)e(N_min)e(N_max)e(N_snp)e(ll)e(iter)e(converged)hap_e(index)0\ L Lfindexstrtorealrangehhapstr_inbase2fill(7@Q[Q7Z( `P7P7u)(7<P=P7P7v)*ZR&@@'e(freq)e(N_snp)\ L Lfindexstrtorealrangehhapstr_inbase2fill(7@Q[Q7Z( `P7P7u)(7<P=P7P7v)*ZR&@@'e(freq)e(N_snp)\%haplotype%phasedhap%unphasedhap%matind%snp%tmpm%index%snpinfo%haploindex%subjsnp%subjects%hapind%hapmat1%hapmat2fallphasedfallunphasedfsidfonesftwosfphasednomisfifcondfsidunphfifunphftmpvfmin2fmax1fwfminindfmaxindfindrangecpanelsumkdiphaseinfoinsnpinreciriiinrowsirtmpinrange_getindex%dihapindiisbase10sortpanelsetuppanelsubview_inbase2fill_sortrowminrowmaxpanelstats_num2binQ(7:77o(7:7z)Q(7:77o(7:7z)Q( 7:(7:7z)Q( 7:(7:7z)Q(7:(7:7z)Q(7:(7:7z)Q(7:(7:7z)(7:7 7-O@>7a P$O'HM>7 71NOC>7 71:::7aPF:P=7a7a7a7a7a7!7"(7)P##! ()7:(, `(.7)#7O `(0#7)#]P#]P #Q[HP7h)#Q[H7h) (#]P #Q[H7h) O(7%PP7#]P=:#]::J#4()7:(, (37) ##7O (37)(, 2(57:(9*(< 9)(> `7a7aNQ[7a)(A P=7aP=7aPQ[=7a))P+)P,:P,7$P##$ + )Q:[#-) :#-)(E PP[7) P:PQ:J)*(P PP[7)(V7) )#(^ PP[7)  P=.)(37)QP:::[P/)Q:[0Q:[1P, 2(h 7<)(lP[7<)(pP[7<)(tPP[7<)(wP[7<)Q7)7&P&P'&7)(z(}7:7(}7:QP[7u)OOQ7 OOQ7 (97:(, P##  ((#71 7#P##  8((#71 7#P]P= 3 P]P= 3 ##&  #]P= 3J  #]P= 3J #V7TP'H  :7u)(z(7:7(z(7:7(7:7u)(7:7u)(7:(, ((7(Q[7u)*Z&@I@@@@'&haptousesnpallphasedsidonestwosifcondphaseinfo \n{txt}Building consistent haplotype pairs:\nalldots. %g\n\nphasehaplobase10allphasedunphased {txt}Subject %g observed genotype:\n{txt}Subject %g haplotype index pairs:\n {txt}Subject %g haplotype pairs:\nr(N_snp)r(N_max)r(N_min)r(N_s)r(N)longidvnamebytehap1_hap2_hap1vnamehap2vnameifopt_ifcond\%haplotype%phasedhap%unphasedhap%matind%snp%tmpm%index%snpinfo%haploindex%subjsnp%subjects%hapind%hapmat1%hapmat2fallphasedfallunphasedfsidfonesftwosfphasednomisfifcondfsidunphfifunphftmpvfmin2fmax1fwfminindfmaxindfindrangecpanelsumkdiphaseinfoinsnpinreciriiinrowsirtmpinrange_getindex%dihapindiisbase10sortpanelsetuppanelsubview_inbase2fill_sortrowminrowmaxpanelstats_num2binQ(7:77o(7:7z)Q(7:77o(7:7z)Q( 7:(7:7z)Q( 7:(7:7z)Q(7:(7:7z)Q(7:(7:7z)Q(7:(7:7z)(7:7 7-O@>7a P$O'HM>7 71NOC>7 71:::7aPF:P=7a7a7a7a7a7!7"(7)P##! ()7:(, `(.7)#7O `(0#7)#]P#]P #Q[HP7h)#Q[H7h) (#]P #Q[H7h) O(7%PP7#]P=:#]::J#4()7:(, (37) ##7O (37)(, 2(57:(9*(< 9)(> `7a7aNQ[7a)(A P=7aP=7aPQ[=7a))P+)P,:P,7$P##$ + )Q:[#-) :#-)(E PP[7) P:PQ:J)*(P PP[7)(V7) )#(^ PP[7)  P=.)(37)QP:::[P/)Q:[0Q:[1P, 2(h 7<)(lP[7<)(pP[7<)(tPP[7<)(wP[7<)Q7)7&P&P'&7)(z(}7:7(}7:QP[7u)OOQ7 OOQ7 (97:(, P##  ((#71 7#P##  8((#71 7#P]P= 3 P]P= 3 ##&  #]P= 3J  #]P= 3J #V7TP'H  :7u)(z(7:7(z(7:7(7:7u)(7:7u)(7:(, ((7(Q[7u)*Z&@@I@@@'&haptousesnpallphasedsidonestwosifcondphaseinfo \n{txt}Building consistent haplotype pairs:\nalldots. %g\n\nphasehaplobase10allphasedunphased {txt}Subject %g observed genotype:\n{txt}Subject %g haplotype index pairs:\n {txt}Subject %g haplotype pairs:\nr(N_snp)r(N_max)r(N_min)r(N_s)r(N)longidvnamebytehap1_hap2_hap1vnamehap2vnameifopt_ifcond` K K Kiiimilen%indmatfbinseqfrevbinseqfpow_num2bin7P$O7P O jP]$P_7P O P]$QP[FQP_Q[FQ_ =M P jP$ HP= 7P_ 7_=M7QP[FQP_Q[FQ_PFK&@` K K Kiiimilen%indmatfbinseqfrevbinseqfpow_num2bin7P$O7P O jP]$P_7P O  P]$QP[FQP_Q[FQ_ =M P jP$ HP= 7P_ 7_=M7QP[FQP_Q[FQ_PFK&@ K KcbiniiinumPO7OO b Fj(p77)l7$`lI73)K&ȩ@@'length of binary vector must exceed %g to represent number %g\n K KcbiniiinumPO7OO b Fj(p77)l7$`lI73)K&@@'length of binary vector must exceed %g to represent number %g\n