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[mmaharish]

integer runit,wunit,maxgenome,maxchr,genomecnt,chrcnt, beginchr,endchr,selfdone,pair,useunit, inst,thisseq,maxseq,framesizechr, maxtask,taskcnt,maxunit,unitcnt,numcore,beginthischr,endthischr,seqptr,numtasks,runnum,showopen,framesize,bexpand15,eexpand15,bexpand24,eexpand24,conflict,tframesize,dmitrysw,unitnumber,reverse,timeseed,ihour,iminute,isecond,deltaseconds,oldseconds,framecnt,gptrcnt,gptr,sortcnt,sortptr,shortframe,unit1,unit2,taskunit1,taskunit2,maxtpos,doblkhist,setc1c2,minsep,smallfrag,thisnumzf,doself,llloop,ulloop,hitcnt,msm1,maxc1c2sep,cposnum,cnegnum,tposnum,tnegnum,tposcontrol,tnegcontrol,cposcontrol,cnegcontrol,bmask,cposbeg,cnegbeg,tposbeg,tnegbeg,smaxtpos,cposend,cnegend,tposend,tnegend,maxgroups,posptrtogptr,negptrtogptr,p4cnt,p4hold,maxp4hold,interaction,cpnumgroups,cnnumgroups,tpnumgroups,tnnumgroups,firstp4file,uposcontrol,unegcontrol,readpttattt,ldist,maxldist,jobnumber,tttsw,mappttsw,integritysw

integer viralsw,viruscnt,mtaskgroup,tmtaskgroupnum,pos1transcript,pos2transcript,pos3transcript,neg1transcript,neg2transcript,neg3transcript,gcposcontrol,gcnegcontrol,gceposcontrol,gcenegcontrol,ncposcontrol,ncnegcontrol,nceposcontrol,ncenegcontrol, pospromoter,negpromoter,pos1clear,pos2clear,pos3clear,tttthisseq,onlyself,neg1clear,neg2clear,neg3clear,silentopen,ldnacnt,iscircular,unitname,notself,cposgroup,cneggroup,tposgroup,tneggroup,aldist,maxctlen,cposoff,cnegoff,tposoff,tnegoff,hc1,hc2,ht1,ht2,p1,p2,p3,bindingstrength,evalct,p4num,p4num1,p4num2,mpunit1,mpunit2,restart,maxpage,skipcnt,intvm,intvi,groupflg,id,nthrds,c10,c20,c30,c40,tlen,llu1,ulu1,firstbadtask,c8,c9,c29


real hhconst,watconst,vanconst


integer*8 pframe1,nframe1,sptr,ssptr

double precision memlimit,bytesperbase,bytesperinst,size,frames,unitsize,unitframes,totalframes,totalopenbases,totalbases,totalctron


parameter(maxseq=12050000, tttthisseq=maxseq)


parameter(maxgenome=5000, maxchr=5000,maxtask=4600000, maxunit=10000, numcore=16,maxtpos=tttthisseq/32, maxpage=3300,smaxtpos=1,maxgroups=100000, maxp4hold=50000, maxldist=1000,maxctlen = 6000)
character*1 chonear,barrier

character*9 ncnames,lineardna

character*40 ncbiname

character*80 genometextname,unittextname

character*40 patheq
character*1 path(40)
equivalence(patheq,path(1))

logical group5,stopprog,group15,group6,group7,singlethread

character*8 genome,chr,genomeofchr,genome1,chr1,genome2,chr2,unitgenome1,unitchr1


common /aa/ memlimit,bytesperbase,bytesperinst,frames(maxchr),unitsize(maxchr),unittextname(maxchr),unitframes(maxchr),size(maxchr),totalframes,totalopenbases,totalbases,iscircular(maxchr),singlethread,runit,wunit,runnum,showopen,readpttattt,genometextname(maxchr),group5,group6,group7,group15,stopprog,path,ncbiname(maxchr),chonear(0:55),genome(maxgenome),chr(maxchr),genomeofchr(maxchr),genomecnt,chrcnt,beginchr(maxgenome),endchr(maxgenome),selfdone(maxchr),pair(maxchr,maxchr),restart,useunit(maxchr),inst(maxchr),framesizechr,taskcnt,taskunit1(maxtask),taskunit2(maxtask),genome1(maxtask),chr1(maxtask),genome2(maxtask),chr2(maxtask),unitgenome1(maxtask),unitchr1(maxtask),unitcnt,beginthischr(maxchr),endthischr(maxchr),seqptr,shortframe,unitname(maxtask),numtasks,skipcnt,intvm,intvi,groupflg,framesize(maxchr),bexpand15(maxchr),eexpand15(maxchr),bexpand24(maxchr),eexpand24(maxchr),conflict(maxchr),tframesize(maxtask),dmitrysw,timeseed,ihour,iminute,isecond,deltaseconds,oldseconds,barrier



common /ab/ thisseq(tttthisseq),framecnt,unitnumber(maxseq),reverse(0:5),doblkhist,setc1c2,minsep,smallfrag,thisnumzf,llloop,ulloop,maxc1c2sep,firstbadtask,jobnumber,tttsw,mappttsw,integritysw,viralsw,viruscnt,silentopen,onlyself,totalctron,notself

common /ac/bmask(32),pos1transcript(smaxtpos),pos2transcript(smaxtpos),pos3transcript(smaxtpos),neg1transcript(smaxtpos),neg2transcript(smaxtpos),neg3transcript(smaxtpos),pospromoter(smaxtpos),negpromoter(smaxtpos),pos1clear(smaxtpos),pos2clear(smaxtpos),pos3clear(smaxtpos),neg1clear(smaxtpos),neg2clear(smaxtpos),neg3clear(smaxtpos)