DELTA 363374 2395 34 SVNW*jk%y >x^uTm8~E@Ek@XEMiꝐb-vK&ݼP !y3yfi6<7Q`IXͪ9wO44`V⨵QDHNkIn(>ID6z,ٿ j5Ki= "Z׆EdxYa]aDBѷףabOvW@"Р^5 V%yx> `yq`(Nhs$ ^m}KV%W]Y+;\/AoD6-eP5~svKikRn2(8i; դ)uWv(Lu@YC3㗜!>`2@Mag+a/3kϮXts8jnx^+Wc7B+bU"Z'྿5KfFxnوP崮?v&Hvp^ĩ퍛zY3G4-Voc{%&ZyíL>D>u57Β.QŽ"n/tƉ? v:}6ʽ+3흛LӮnG|RmMA\;{IENDREP DELTA 271305 89823 17 SVNnmmgz) = 8038d2b94078ba918e97785fc7497252139029281000f1c54ff9dd1ec70e05fc SIZE (consed_linux.tar.gz) = 34390726 ENDREP DELTA SVNXfXXx^To0~^T[0S[IL!Ub&vd;Vӵ 1M1;wgi,ϲN:(-^tz1"~|?~= E^u) :'h#4X>-Aݱ]lL%<۰@t\O t #)ؙ0.@ZX$h'TX(&T%pP!! j"CM\4Iv0hоqck8l~%gL6韜 VwTumҒeVT<ro- ~Ph50'9^rtrjQB$VB)YX D"2*+ YScܻ9hg~ WsQZvY`N^RJ5Lk,yX[ x zSohp!5wrwX؊O,a_i]D{T3UCh|sCh$\{OVlK]L=YMm\Ml'/F LJij2^%8E -h+ѶF/:va7a}6hrkn}Kaj.3 1J/zy=ң8=g}2E&a Zm&0=[>JMkXֽ(uy$M\KOSUٗƏ{*ENDREP DELTA 213590 2864 506 SVNCJ . ,5,14-02-12 05:28:45.000000000 +0900 +++ scripts/phredPhrap 2014-06-22 03:07:33.000000000 +0900 @@ -217,7 +217,7 @@ #$solexaDirPath = "../solexa_dir"; #$sffDirPath = "../sffENDREP DELTA SVNe7eex^1O0wDM n LM.UWN{H[{Zn9Aj-bR9*~$y]O/oIZ: J!wn`P2HBZs7>]z?l|F yAU!JV#8[n)`䞐5eVg;l[Vv ݎgȏO4y3/}P ңcKtN!-Z=QC>FCr<}-}3q g1W%w'M!WncsUd*~?Qø9ENDREP DELTA 353593 102 24 SVN*7UqGFDef_x^[o08xK.$CťQ.i`-J mnKef/'~ɹs&8өPw<6ʭˮ~r Ło n7R`q,w\l8,{j.f[ V@G׈N#z2S~ک91^A'Co(k FƕbJY1=gu!jX0 Ϲ3k]0A-Th1BQW~0{x;.Ldԓ/%Y8 o&>t e4p&G]t!}8Eog!hC9O=?wƎ~;Uk<[_: \ʩRJךlI^0#>*X ٘|:FKR `zV?VHm<6BSBSRJS@Y}lz+wNrmc99#8M. 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QVb*|p͹B.-T9EY`2`LG)$$( ;2?F^0LawN*(N)JHýq:ϞNˡ+|L~OENDREP DELTA SVN%'%%--- ./calf_utils.c.orig 2008-11-04 23:21:50.000000000 +0100 +++ ./calf_utils.c 2014-08-02 12:39:30.000000000 +0200 @@ -28,6 +28,8 @@ extern void *malloc(), *realloc(); +void read_type_3(File_stat *, int); + append_file_stat(file_name) char *file_name; { @@ -110,6 +112,7 @@ get_record_header(file_stat); } +void read_type_3(file_stat, new_rec_flag) File_stat *file_stat; int new_rec_flag; ENDREP DELTA SVN--- ./call_subs.c.orig 1999-01-17 00:42:56.000000000 +0100 +++ ./call_subs.c 2014-08-02 12:39:30.000000000 +0200 @@ -26,15 +26,13 @@ extern Parameters *parameters; +void call_write_exp_files(n_sing, n_contigs, contig_ptrs) int n_sing, n_contigs; Contig **contig_ptrs; { #if defined(GCPHRAP) write_exp_files(n_sing, n_contigs, contig_ptrs); - return; -#else - return; #endif } ENDREP DELTA SVNDyDDx^PN0<#G۔?,g[R'N'5 }xEQ@䨌.g.wS`@EMy}8Ӏ!߰ r`?`m 8G m3c*7|ͻiLU u4D 2@n{VX1w8҇<`e)/5j(I1 e2ԽiƪVEMU=}?Y{.ENDREP DELTA SVNkmkk--- ./contigs.c.orig 2008-11-11 22:56:27.000000000 +0100 +++ ./contigs.c 2014-08-02 12:39:30.000000000 +0200 @@ -2115,6 +2115,7 @@ contig1->base_segment = previous_base_segment; } +void write_contigs() { char *our_alloc(); ENDREP DELTA SVNXbXXx^n0E+FIxDm_,*rb,6$aѪgC0fEPU/"dG!I,{_=VN0I0 x|'hX.=T5/t]&W+S ؜khKsG-(=Hh\<ޙO^ENDREP DELTA SVNBDBB--- ./names.c.orig 2007-11-06 23:03:53.000000000 +0100 +++ ./names.c 2014-08-02 12:39:30.000000000 +0200 @@ -30,6 +30,8 @@ #define MAX_SUBCLONE_HIST 101 +void print_contig_chains(); + set_delims() { subclone_delim = parameters->subclone_delim; @@ -1014,6 +1016,7 @@ /* greedy algorithm for finding chains of contigs */ /* NEED TO LOOK SYSTEMATICALLY FOR CIRCULAR CHAINS, AND BREAK THEM */ +void print_contig_chains() { Link *link; ENDREP DELTA SVN--- ./nodes.c.orig 2008-08-31 03:44:15.000000000 +0200 +++ ./nodes.c 2014-08-02 12:39:30.000000000 +0200 @@ -31,6 +31,8 @@ extern Parameters *parameters; /* exported */ extern double *scaled_err_probs; int *contig_graph_weights; + +void nr_tarjan(int); set_contig_graph_weights() { @@ -679,6 +681,7 @@ curr_state->calling_point = calling_point; } +void nr_tarjan(k) int k; { ENDREP DELTA SVNdXddx^Uَ0}jcHH2JEԗ>WEVYRvb#H]ιq`x\r;.^`4F IaY!LFf ݽ;X{ SX `E#V$:G;Iy#ڕ,NwLP#!".9gm$|^Vm0G2%HQN+ʅƜ`//.rZEy-vPxx4w'.b+bcO>HEyPW"iq[۳: IfT1Z=CaZPC=ri383;O7%_ܯr: 6[|w ~|LlW0Nمɞ7 M6ٜ<~Hkpmovy?W7H}lH6%Iy֫ymx|y}{X7G8lCENDREP DELTA SVNr%rrx^Umo0[B!@ZS[iغNPd,:+wv^^.>y98>izd'< Bs?8q:.q]ԧ<{vu`@߷#_\X+x\(X|IUGC l=K,Jf|mX,y&aEE ,}!6dɄʡ}jyx 8+xXo,s0yjE7TBۆaٰ3\W&Hul a^зg*b[ Xe<T:A0AI.o{uswwWVo# &e8yIְT&\M|0\.4pCI,fZtb"6ElN7mǽpߒ+zJT/T4ӔD-JCZN%{d2Jf̼df4 5">ʊG!J)>5Zlwhv3дBgg@*R|3F]y%hC;:q?r|kC|GF`OIP2&ZE֞孕߬rc \ UDS%op~"Trc714S-hҤͫ."k'o)UH\sq2[Bf3#EOs?)5tjVr%զ3.nFoShR솀댇aU<'dV/bDENDREP DELTA SVN4644--- ./readin.c.orig 2008-11-11 20:33:41.000000000 +0100 +++ ./readin.c 2014-08-02 12:39:30.000000000 +0200 @@ -31,6 +31,7 @@ /* read in sequence files, initialize array of aligned read info, and log file of ancillary information, and find pairwise matches */ +void readin_and_match() { File *file; ENDREP DELTA SVN   --- ./segments.c.orig 2008-07-30 19:14:13.000000000 +0200 +++ ./segments.c 2014-08-02 12:39:30.000000000 +0200 @@ -112,6 +112,7 @@ return head; } +void print_segments(head, index, complement) Segment *head; int index; @@ -128,6 +129,7 @@ } } +void old_print_segments(head, index1, index2, offset, rel_orient) Segment *head; int index1, index2, offset; ENDREP DELTA SVNx^Ak@_1ǤY (-B9bl*\J{]c B t.ͼF[PC2&Ffu"G$9B|p0e.qGIQ6HBQ^a/jpbp2;7`Ng+eZ)Tըf)J +u@ΪGurgUdg*ILQ7OeZJLUSvB~9[oW'%B:Ymfa}ENDREP DELTA SVN|~||--- ./weibull.c.orig 2008-07-29 20:06:24.000000000 +0200 +++ ./weibull.c 2014-08-02 12:39:30.000000000 +0200 @@ -77,6 +77,7 @@ z_cutoff = Z_CUTOFF; } +void update_hist(score_entry, z_flag) Score_entry *score_entry; int z_flag; @@ -103,6 +104,7 @@ score2_sums[length] += score * score; } +void prune_hist(score_entry) Score_entry *score_entry; { ENDREP DELTA SVNA0AAx^}T]:}󸐰$t]}tǪL2 NmgYzu{N, lqO&.}~Iq'i iiz1a#O$N!I׳,x~1z0[C+$oqd\hƵd'N4'4n:\ҚQ_VԬm/,;MI ,j.|5߯V;_KwمUq](`%Q܂90,*cjG~I%|f5i>FKߤcP>Bka>}ae+xzӡ-ATKxNcXDPs? -|C)[iԢeevPZ-Pmj&C͖o1F KjUIVSUW^u1[Qڛ/pC0׈G q$^TwH몯>NSߩ]R`C2!6nJ}pkõ5ѵBq*` M}ozEe)r2?k,li1io4>_L%1gFNp]uSGN U6 cⱌ"&Cګ#>rs.W>G(Av{qqyUҶֳfv4pMv@2}ۍ! 45H:׆u{>N~VC|k4 x8`AK|{$j~&%WLd , ENDREP DELTA SVNfgff@mode 111 bin/calf_merge bin/pcluster bin/cross_match bin/loco bin/phrap bin/phrapview bin/swat @mode ENDREP DELTA 353593 154 24 SVNIHd bn+SUB_FILES= pkg-messageARIES= phred daev DATADIR= ${PREFIX}/etc/PhredPar DATAFILES= phredpar.dat PORTDOCS= NEWS PHRED.DOC DAEV.DOC STAGEDIR}${PREFIX}/bin/ .endfor @${MKDIR} ${STAGEDIR}${DATADIR} .for f in ${DATAFILES} @${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}${DATADIR}/${f}.sample .endfor @${MKDIR} ${STAGEDIR}${DOCSDIR} .for f in ${PORTDOCS} @${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}${DOCSDIR} .endforENDREP DELTA SVN,.,,----------------------------------------------------------------------------- You must set PHRED_PARAMETER_FILE environment variable. 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