all his other posts seem to have been

Practice exercises, but I am trying to simply understand how to go about solving since I do not understand the question. So far I have :

foreach my $id (@{$ids}) {
    my $alignments = $sam -> get_features_by_location(-seq_id => $transcript_id, -iterator => 1);

    while (my $alignment = $alignments -> next_seq) {
        my $read_name = $alignment -> query -> name;

        if (exists($global_read_occurrences{$read_name})) {
            $global_read_occurrences{$read_name}++;
        }
        else {
            $global_read_occurrences{$read_name} = 1;
        }
    }
}