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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

Output:

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

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In reply to Re^2: Discard if present within other coordinate range by BrowserUk
in thread Discard if present within other coordinate range by jnarayan81

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