#!/usr/bin/perl -w 


@files = qw(sr_2AB_1_BC1_sorted.bed
sr_2AB_2_BC2_sorted.bed
sr_2AB_T_BC3_sorted.bed
sr_45_2_BC5_sorted.bed
sr_45a_1_BC4_sorted.bed
sr_45b_1_BC6_sorted.bed
sr_91a_1_BC7_sorted.bed
sr_91a_2_BC8_sorted.bed
sr_91b_1_BC9_sorted.bed
sr_91b_2_BC10_sorted.bed);

foreach $f (@files){
#$f="test";
open(IF,"$f");
open(B4,">b4.$f");
open(EX,">ex.$f");
open(IN,">in.$f");
while($a=<IF>){
#print $a;
chomp($a);
@b = split(/\t/,$a);
$nexon = $b[9];
@sizes = split(/,/,$b[10]);
@starts = split(/,/,$b[11]);
print B4 "$b[0]\t$b[1]\t$b[2]\t$b[3]\t$b[4]\t$b[5]\n";
#splRep	830	937	m150909_135227_42146_c100889372550000001823187103261633_s1_p0/546/ccs	0	+	830	937	255,0,0	1	107	0
#splRep	830	3294	m150909_135227_42146_c100889372550000001823187103261633_s1_p0/3588/ccs	0	+	830	3294	255,0,0	2	108,214	0,2250
for($i=0;$i<$nexon;$i++){
$exstart  = $b[1] + $starts[$i];
$exend = $b[1] + $starts[$i] + $sizes[$i];
print EX "$b[0]\t$exstart\t$exend\t$b[3]\_$i\t$b[4]\t$b[5]\n";

if($i>0){
$instart = $b[1] + $starts[$i-1] + $sizes[$i-1];
$inend = $b[1] + $starts[$i];
print IN "$b[0]\t$instart\t$inend\t$b[3]\_$i\t$b[4]\t$b[5]\n";
#print "$b[0]\t$instart\t$inend\t$b[3]\_$i\t$b[4]\t$b[5]\n";

}
}

}
close(IF);
close(EX);
close(IN);
close(B4);
#exit;

system("sort -k1,1 -k2,2n b4.$f > tmp.bed");
system("mv tmp.bed b4.$f ");
system("bedtools genomecov -g chrom.sizes -bga -i b4.$f > b4.$f.bedgraph");

system("sort -k1,1 -k2,2n in.$f > tmp.bed");
system("mv tmp.bed in.$f ");
system("bedtools genomecov -g chrom.sizes -bga -i in.$f > in.$f.bedgraph");

system("sort -k1,1 -k2,2n ex.$f > tmp.bed");
system("mv tmp.bed ex.$f ");
system("bedtools genomecov -g chrom.sizes -bga -i ex.$f > ex.$f.bedgraph");

}