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#!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 partitions.gff join_within_dist\n";
my $partitions_gff = $ARGV[0] or die $usage;
my $join_within_dist = $ARGV[1] or die $usage;
my @prev_line;
open (my $fh, $partitions_gff) or die "Error, cannot open file $partitions_gff";
while (<$fh>) {
chomp;
my @x = split(/\t/);
if (!@prev_line) {
@prev_line = @x;
next;
}
if ($x[0] ne $prev_line[0]
||
$x[3] - $prev_line[4] > $join_within_dist) {
print join("\t", @prev_line) . "\n";
@prev_line = @x;
}
else {
# same contig and within distance
$prev_line[4] = $x[4]; # update right end.
}
}
print join("\t", @prev_line) . "\n" if @prev_line;
exit(0);
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