E00489:44:HNNVYCCXX:3:1101:24890:5616   99      22      16052014        150M
E00489:44:HNNVYCCXX:1:1110:21704:27345  99      22      16052044        150M
E00489:44:HNNVYCCXX:1:1217:2372:69519   163     22      16052044        150M
E00489:44:HNNVYCCXX:3:2123:8948:16779   99      22      16052044        150M
E00489:44:HNNVYCCXX:2:2213:2920:25534   147     22      16052054        146M4S
E00489:44:HNNVYCCXX:2:2206:5020:71717   83      22      16052055        145M5S
E00489:44:HNNVYCCXX:4:2206:12642:40829  99      22      16052056        144M6S

#!/bin/perl

#initialize hashes
my %softhash;
my %IDhash;
my $file1Name = $ARGV[0] . 'all_sc_positions.txt';
my $file2Name = $ARGV[0] . 'edge_sc_positions.txt';
open(my $fh_all, '>', $file1Name);
open(my $fh_edge, '>', $file2Name);

#for each line
while (my $line = <STDIN>) {

    #read in line and parse
    chomp($line);
    my @a = split("t", $line);
    my $start = $a[3];
    my $cigar = $a[4];
    my @b = split(/[A-Z]/, $cigar);# keeps track of numbers
    my @c = split(/[0-9]*/, $cigar); #keeps track of letters
    my $loc = $start; #distance from start of read
    my $var_start;
    my $var_end;

    #loop over type of alignment in cigar string, build hashes of candidate locations
    for (my $i = 0; $i <= $#c; $i++) {

        #if there is softclipping or an indel, find the location and store in hash
        if ($c[$i] eq "S" || $c[$i] eq "I" || $c[$i] eq "D") {

            #find softclipping location
            if ($i == 1) {

                $var_start = $start - $b[0];
                $var_end = $start;

                if ($c[$i] eq "S") {

                    for (my $pos = $var_start; $pos < $var_end; $pos++) {
                        $softhash{$a[2]}{$pos}++;
                    }

                    $var_start = $var_end - 1;
                    $var_end = $var_start;
                }

            } else {

                for (my $j = $i-2; $j >= 0; $j--) {# subtract 2 from i, because the first value from c will always be empty
                    $loc = $loc + $b[$j];
                }

                $var_start = $loc;
                $var_end = $loc + $b[($i-1)];

                if ($c[$i] eq "S") {

                      for (my $pos=$var_start; $pos<$var_end; $pos++) {
                           $softhash{$a[2]}{$pos}++;
                      }

                      $var_end = $var_start;
                }
            }

            $IDhash{$a[2]}{$var_start}{$var_end}{$c[$i]}++;
        }
    }
}

#write out edge features
foreach my $key_chr (sort(keys %IDhash)) {

        foreach my $key_start (sort { $a <=> $b } (keys %{  $IDhash{$key_chr}  })) {

                foreach my $key_end (sort { $a <=> $b } (keys %{  $IDhash{$key_chr}{$key_start}  })){

                    print $fh_edge "$key_chrt$key_startt$key_endt";
                    my $sum = $IDhash{$key_chr}{$key_start}{$key_end}{I} + $IDhash{$key_chr}{$key_start}{$key_end}{D} + $IDhash{$key_chr}{$key_start}{$key_end}{S};
                    print $fh_edge "$sum,";

                    for my $l ('S','I','D') {

                    if (defined($IDhash{$key_chr}{$key_start}{$key_end}{$l})) {
                         print $fh_edge  "$IDhash{$key_chr}{$key_start}{$key_end}{$l},";
                    } else {
                        print $fh_edge "0,";
                    }
            }

            print $fh_edge "n";
        }
    }
}

#write out "all" features
foreach my $key_chr (sort(keys %softhash)) {

        foreach my $key_pos (sort { $a <=> $b } (keys %{  $softhash{$key_chr}  })) {

             print $fh_all "$key_chrt$key_post";
             print $fh_all "$softhash{$key_chr}{$key_pos}n";
        }
}