Re^2: Discard if present within other coordinate range

Eg. Assuming that you have upto a few hundred million IDs (and enough memory to accommodate 4 bytes per ID), and that the input file is already sorted by range (as I believe is typical for this type of data; if not sort it it first using your system sort utility):

#! perl -slw
use strict;

my @ids;
my $tally = chr(0);

while( my( $id, $start, $end ) = split ' ', <DATA> ) {
    my $startId = vec( $tally, $start, 32 );
    my $endId   = vec( $tally, $end,   32 );
    next if $startId and $endId and $startId == $endId;
    push @ids, $id;
    my $idn = @ids;
    vec( $tally, $_, 32 ) = $idn for $start .. $end;
    print "$id $start $end";
}

__DATA__
SEQ2 99 140
SEQ2 100 150
SEQ2 101 149
SEQ2 120 130
SEQ2 120 230
SEQ1 145 244
SEQ1 200 300
SEQ1 201 299
SEQ1 225 275
SEQ1 250 399
[download]

Output:

C:\test>1182245.pl
SEQ2 99 140
SEQ2 100 150
SEQ2 120 230
SEQ1 145 244
SEQ1 200 300
SEQ1 250 399
[download]

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