/usr/bin/chrom_sizes.pl is in libbio-samtools-perl 1.43-1+b2.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 | #!/usr/bin/perl
use strict;
use Bio::DB::Sam;
my $bamfile = shift or die "Usage: $0 <bamfile>\nOutput a chrom_sizes file.\n";
my $bam = Bio::DB::Sam->new(-bam=>$bamfile) or die "Couldn't open $bamfile";
my @seqids = $bam->seq_ids;
for my $s (sort @seqids) {
my $len = $bam->length($s);
print join("\t",$s,$len),"\n";
}
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