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1 | Search.setIndex({envversion:46,filenames:["howto","index","pbalign","pbalign.alignservice","pbalign.forquiverservice","pbalign.tools","pbalign.utils"],objects:{},objnames:{},objtypes:{},terms:{"default":0,"function":0,"import":0,"new":0,access:0,accord:0,accuraci:0,activ:0,advanc:0,against:0,algorithm:0,algorithmopt:0,align:[0,2],alignerscor:0,alignservic:2,aligorithm:0,all:0,allbest:0,allow:0,alreadi:0,also:0,anchor:0,api:0,apt:0,arg:0,argument:0,avail:0,base:0,basic:0,bax:0,been:0,befor:0,below:0,best:0,between:0,bin:0,bioinformat:0,blasr:[0,2],blasrscor:0,blob:0,bowti:[0,2],bowtie2:0,build:0,bundl:0,can:0,cannot:0,ccssequenc:0,chang:0,circular:0,clone:0,cluster:0,cmp:0,cmph5tool:0,code:0,com:0,command:0,compar:0,compat:0,compress:0,config:0,configfil:0,consensu:0,consum:0,contain:0,content:1,convert:0,creat:0,createchemistryhead:2,criteria:0,current:0,debug:0,debugg:0,defin:0,deposit:0,dev:0,directli:0,directori:0,distanc:0,distinguish:0,diverg:0,doe:0,download:0,each:0,edit:0,editdist:0,either:0,evalu:0,even:0,example_read:0,example_ref:0,execut:0,exit:0,exitcod:0,extens:0,extractunmappedsubread:2,fals:0,fasta:0,fastabasedalign:2,filenam:0,fileutil:2,filter:0,first:0,fofn:0,follow:0,format:0,forquiv:[0,2],forquiverservic:2,from:0,gener:0,genom:0,get:0,git:0,github:0,gmap:2,googl:0,h5py:0,h5repack:0,have:0,hdf5:0,hdf5_tool:0,hdfgroup:0,help:0,hit:0,hitpolici:0,http:0,inform:0,initi:0,input:0,inputfilenam:0,integ:0,interv:0,isol:0,length:0,level:0,libhdf5:0,line:0,list:0,load:0,loadchemistri:2,loadpuls:[0,2],machin:0,mai:0,manipul:0,map:0,mask_aligned_read:2,master:0,match:0,maxdiverg:0,maxhit:0,maximum:0,mean:0,messag:0,minaccuraci:0,minanchors:0,minimum:0,minlength:0,multipl:0,must:0,my_env:0,name:0,namespac:0,ncandid:0,need:0,none:0,nosplitsubread:0,note:0,nproc:0,number:0,numpi:0,object:0,onli:0,order:0,org:0,otherwis:0,out:0,output:0,outputfilenam:0,pacbio:0,pacificbiosci:0,packag:0,part:0,pass:0,pbalignrunn:0,pbcore:0,pbh5tool:0,pbtool:0,percentag:0,permiss:0,pip:0,pleas:0,pls2fasta:0,plx:0,polici:0,posit:0,pre:0,preprocess:0,print:0,process:0,product:0,profil:0,program:0,progutil:2,provid:0,pseudo:0,puls:0,pypi:0,python2:0,qualiti:0,quiver:0,random:0,randombest:0,read:0,readm:0,refer:0,referencepath:0,referenceupload:0,region:0,regiont:0,releas:0,remov:0,repack:[0,2],repositori:0,rgnh5io:2,root:0,runtim:0,sam:0,samfilt:0,samtoh5:0,save:0,scm:0,score:0,scorecutoff:0,scorefunct:0,scratch:0,script:0,sdptuples:0,seed:0,select:0,sequenc:0,serial:0,server:0,session:0,show:0,site:0,size:0,smrtanalysi:0,sort:[0,2],sourc:0,span:0,specif:0,specifi:0,split:0,start:0,subread:0,sudo:0,support:0,system:0,tabl:0,tag:0,tempfileutil:2,templat:0,temporari:0,test:0,them:0,therefor:0,thi:0,thread:0,through:0,time:0,tmpdir:0,treat:0,ubuntu:0,uninstal:0,unlei:0,upload:0,usecc:0,useccsal:0,useccsdenovo:0,user:0,util:2,valu:0,verbos:0,version:0,virtualenv:0,visit:0,want:0,which:0,whole:0,within:0,worst:0,www:0,you:0,your_movi:0,your_refer:0,yourself:0,zero:0},titles:["How to install and run pbalign","pbalign","pbalign package","pbalign.alignservice package","pbalign.forquiverservice package","pbalign.tools package","pbalign.utils package"],titleterms:{align:3,alignservic:3,background:0,blasr:3,bowti:3,content:[2,3,4,5,6],createchemistryhead:5,data:0,environ:0,exampl:0,extractunmappedsubread:5,fastabasedalign:3,file:0,fileutil:6,filterservic:2,forquiv:4,forquiverservic:4,gmap:3,how:0,instal:0,instruct:0,librari:0,loadchemistri:[4,5],loadpuls:4,manual:0,mask_aligned_read:5,modul:[2,3,4,5,6],option:[0,2],packag:[2,3,4,5,6],pbalign:[0,1,2,3,4,5,6],pbalignfil:2,pbalignrunn:2,progutil:6,python:0,repack:4,requir:0,rgnh5io:6,run:0,servic:2,set:0,softwar:0,sort:4,step:0,submodul:[2,3,4,5,6],subpackag:2,tempfileutil:6,tool:[0,5],usag:0,util:6,virtual:0,your:0}})
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