function cc(s,ff){ n=split(s,a," "); re=""; for (i=ff;i<=n;i++){re=re a[i];} print n" "re" "id return(re); } function storeseq(){ l=length(cig); lp=rstart; for (i=28;i<=l;i++){ # x=substr(rseq,i,1); if ( (i-27)%11 == 0 ){ # printf("_"); } else{ rs[p]=substr(rseq,i,1); rq[p]=substr(qual,i,1); rc[p]=substr(cig,i,1); if (substr(ref,i,1)!="-"){; if (lp==110){pp[0]=p;} if (lp==111){pp[1]=p;} lp++; } p++; # printf("%c",x); } } # printf("\n"); } { if ($1=="Read-Name"){id=$3;} if ($1=="Strand"){str=$3;} if ($1=="Start"){start=$3;} if ($1=="End"){end=$3; if ( (start<=110) && (end>=111) ){r=1;p=0;pp[0]=-1;pp[1]=-1;} # print start,end,r } if (r==1) { if ($1=="Read"){ rseq=$0;# print $0; getline; #Middle getline; ref=$0;#print $0;#Ref rstart=0+substr($2,2,length($2)-2); #print rstart" "str;} getline; cig=$0;#print $0; #Cigar getline; qual=$0;# print $0; #Qual getline; refpos=$0; storeseq(); } if ($1=="Tags"){ if ((pp[0]>=0)&&(pp[1]>=0)) { if (rc[pp[0]+1]=="I"){ is=pp[0]+1;ie=pp[1]; print ">"id for (i=is;i