DELTA 467553 0 27 SVN' A]2 freebayesENDREP DELTA SVN}>}}x^mU]o8}ƿ @d/:ۇ8c3)eI3}@=>ھ|q؝_FhXÙ;(")91=]b\cqPzܨ6u4b>@+'fCo_nUlh1tgwD eN{VD8*︎quYrDxˤerEhܹyk>a@cV"d Jjlv1Ȟk DBBI $=P0H6WXHj 3L\LOi} 2#SOKÆ$LAV{e3*ikr W;A;>1ۍ඗P1,Q d(:H2;Ϩ5̌X9Q z$6J 쌆8~F4\tR\ǡu݊ O *%Dx0NHi;4 Q^N5Ad  Xp) "ڐ d( V Rn贊rˢV)kV0<6 .KEv`3R1+`fN:!rTHuH iLk^}w`_{W7ڲ8eᇏ5ٰ?{r&5 BԬi[6d`%1on?C3o'ǁ>EĿƭT MF)Jl}u7/sK/`7͌Qڷ.Xd[-pq[{uaId. LNr; LJ}A2{Cl]xAuMc c 5+m*$$0*_gpE?jvmA?\5;IVz ЀB[zs=N7bޮ6&z+UBU.qjm?WENDREP DELTA SVN5t55x^Vn7 +rlcDRr P9RP"eoΦޭmd== 0{"{W_\yg?>a&._>ϕ}ﮖy//wp/o?L82@nDCpj6! ^6P Rw~}qR&lgruoKM_j+0HVG g{'nO d3.:tk'wBipoGNmu)3ΌᵰӧTFENTgbGiQPghj:LgwVN7e9Rhi;!"60DBQikAI282G34͹|Mi"lzsF J6lEr3U<5&*bK!; 'V6[qam]›Jn9[`zh<¹s$+&>=}PtIT!fQ^}K5EG\RsxNК\usX(_jb9W+jy"Dw.dnqvNeº1&pFnIgWa:Y=Kâ6 3c62=̕?͸0V0k.\kPMB}vCLjHki4fΈ< 5~o9\Ը؍_"AhQ|()%IH:XXt%E>ƄAg^O͟>,䯆!!`}Du(~T ըaN&džRKY&ߧ %c0"VG"Mz%%ZFjbCXP c71! m0Hb-?_ENDREP DELTA SVN?x^QMK1=o~ŠiTTOқ Mg&-E&kk.!/^1R K82Vd:Ng0Ɠp鞤i$Л9y.VZ@m$DY>˻LJ!8&@"?\֢u/RQIh聾A&cmжF7 YasCF5 \Z/iqmG'30e $M.?=ȳk7{ZtcjMjQl+`L5U}Xu4,dk4P:}}~wRhy]| ?ŧENDREP DELTA SVNBDBB--- SeqLib/bwa/Makefile.orig 2018-03-23 18:47:04 UTC +++ SeqLib/bwa/Makefile @@ -1,8 +1,8 @@ -CC= gcc +CC ?= gcc #CC= clang --analyze -CFLAGS= -g -Wall -Wno-unused-function -O2 +CFLAGS ?= -g -Wall -Wno-unused-function -O2 WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS -AR= ar +AR ?= ar DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC) ## moved is.o bwtiindex.o rope.o to LOBJS LOBJS= utils.o kthread.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o \ ENDREP DELTA SVNlnll--- SeqLib/bwa/bwt_lite.c.orig 2018-03-23 18:49:48 UTC +++ SeqLib/bwa/bwt_lite.c @@ -1,6 +1,7 @@ #include #include #include +#include #include "bwt_lite.h" #ifdef USE_MALLOC_WRAPPERS ENDREP DELTA SVNhjhh--- SeqLib/bwa/bwtgap.h.orig 2018-03-23 18:49:18 UTC +++ SeqLib/bwa/bwtgap.h @@ -3,6 +3,7 @@ #include "bwt.h" #include "bwtaln.h" +#include typedef struct { // recursion stack u_int32_t info; // score<<21 | i ENDREP DELTA SVNVXVV--- SeqLib/bwa/kthread.c.orig 2018-03-23 18:48:35 UTC +++ SeqLib/bwa/kthread.c @@ -1,6 +1,7 @@ #include #include #include +#include /************ * kt_for() * ENDREP DELTA SVN(*((--- SeqLib/fermi-lite/Makefile.orig 2018-03-23 18:50:25 UTC +++ SeqLib/fermi-lite/Makefile @@ -1,6 +1,6 @@ -CC= gcc -CFLAGS= -g -Wall -O2 -Wno-unused-function #-fno-inline-functions -fno-inline-functions-called-once -CPPFLAGS= +CC ?= gcc +CFLAGS ?= -g -Wall -O2 -Wno-unused-function #-fno-inline-functions -fno-inline-functions-called-once +CPPFLAGS ?= INCLUDES= OBJS= kthread.o misc.o \ bseq.o htab.o bfc.o \ ENDREP DELTA SVNLdLLx^Rmo0\~IۇMM%)&Y*fmhUU!{{!?Wb;8hUu(J3< qp %lϲm?k68awlf'XD&AGp$KH>tܹo FĭHQLﮂ&6gX|اEܨ׸H䆫K,ײ{=xڢ=}C;ЀK+*UF F;,\ #퓃&X< 1ԲmMqC*Sg)#Q?8 HBܥMv+-=(-Eu%5,t6I=]!&h8^Wa1>/ ۩Z `bglخ)SƐ"#φ Iցg\w%X{'dE6|~?>ygJ_k;zܠQrPT)/%^Q%ȍlћȽ9 N }\^9 #ج x2ϰ.sP^Œ+e e## ʴhpz~qΎ_