adding a quick bit of code to check for bam alignments

misc-scripts/datafiles/first_bam_alignment.pl

+#!/usr/bin/env perl
+
+package Script;
+
+use strict;
+use warnings;
+
+use Bio::DB::Sam;
+
+sub run {
+  my ($class) = @_;
+  my $self = bless({}, $class);
+  $self->args();
+  $self->check();
+  $self->setup();
+  $self->process();
+  return;
+}
+
+sub args {
+  my ($self) = @_;
+  my $opts = {
+    port => 3306
+  };
+  GetOptions(
+    $opts, qw/
+      file=s
+      help
+      man
+      /
+  ) or pod2usage(-verbose => 1, -exitval => 1);
+  pod2usage(-verbose => 1, -exitval => 0) if $opts->{help};
+  pod2usage(-verbose => 2, -exitval => 0) if $opts->{man};
+  $self->{opts} = $opts;
+  return;
+}
+
+sub opts {
+  my ($self) = @_;
+  return $self->{'opts'};
+}
+
+sub check {
+  my ($self) = @_;
+  my $o = $self->opts();
+
+  my @required_params = qw/file/;
+
+  foreach my $r (@required_params) {
+    if (!$o->{$r}) {
+      pod2usage(
+        -message => "-${r} has not been given at the command line but is a required parameter",
+        -verbose => 1,
+        -exitval => 1
+      );
+    }
+  }
+  return;
+}
+
+sub process {
+  my ($self) = @_;
+  my $file = $self->opts->{file};
+  die "Cannot find file" unless -f $file;
+  my $bam = Bio::DB::Bam->open($file);
+  my $header = $bam->header();
+  my $a = $bam->read1();
+  my $query_start  = $a->query->start;
+  my $query_end    = $a->query->end;
+  my $query_dna    = $a->query->dna;
+  printf('%s:%d-%d', $query_dna, $query_start, $query_end);
+  print "\n";
+  return;
+}
+
+
+Script->run();
+
+1;
+__END__
+
+=pod
+
+=head1 NAME
+
+first_bam_alignment.pl
+
+=head1 SYNOPSIS
+
+  #BASIC
+  ./first_bam_alignment.pl -file FILE [-help | -man]
+  
+  #EXAMPLE
+  ./first_bam_alignment.pl -file my.bam
+  
+=head1 DESCRIPTION
+
+A script which returns the first region with BAM data in it. Used as a way of sanity checking that
+a BAM has some kind of alignment available.
+
+=head1 OPTIONS
+
+=over 8
+
+=item B<--file>
+
+The location of the BAM
+
+=item B<--help>
+
+Help message
+
+=item B<--man>
+
+Man page
+
+=back
+
+=head1 REQUIREMENTS
+
+=over 8
+
+=item Perl 5.8+
+
+=item Bio::DB::Bam
+
+=back
+
+=end
+