On Tue, 13 Sep 2011 04:54:40 -0700, Lemon wrote:
> I have some segments start and end position on a reference sequence, I
> want to calculate the uncoverage region for the reference;
>
> for example: reference sequence length= 100,
>
> name [start,end]
> segment 1 [1,20]
> segment 2 [2,28]
> segment 3 [50,100]
> segment 4 [5,38]
>
> so uncover region = [38,49]
>
>
> now I already have %pos{start}=end structure for those segment position,
> could somebody give a good method?
By the usual definition the uncovered region is [39,49]. Here's an
approach:
$ cat differ
#!/usr/local/bin/perl
use strict;
use warnings;
use Set::IntSpan; # http://search.cpan.org/perldoc?Set%3A%3AIntSpan
my ($diff, @sets) = map { Set::IntSpan->new( $_ ) }
qw(1-100 1-20 2-28 50-100 5-38);
$diff -= $_ for @sets;
print "$diff\n";
$ ./differ
39-49
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