GitLab

Created by: keiranmraine

The docs need rewording for 'query' to make it very clear that the coordinate format is 1-based for start and stop, unlike the legacy Tabix module (which was 0-based start).

It is also inaccurate to say that to retrieve 1 coordinate that a string of '12:5000000-5000001' is required:

$ zcat test.bed.gz
1   9   10  .   stuff
1   10  11  .   more

$ perl htsTabix.pl test.bed.gz 1 9 10
1   9   10  .   stuff
$ perl htsTabix.pl test.bed.gz 1 9 11
1   9   10  .   stuff
1   10  11  .   more
$ perl htsTabix.pl test.bed.gz 1 10 11
1   9   10  .   stuff
1   10  11  .   more
$ perl htsTabix.pl test.bed.gz 1 11 11
1   10  11  .   more
$ perl htsTabix.pl test.bed.gz 1 12 12

script:

use strict;
use warnings;
use Bio::DB::HTS::Tabix;

my $file = shift @ARGV;
my $tabix = Bio::DB::HTS::Tabix->new(filename => $file);

my $iter = $tabix->query(sprintf '%s:%d-%d', @ARGV);
while(my $l = $iter->next) {
  print $l, "\n";
}