<commit_before>#!/usr/local/ensembl/bin/perl

use strict;
use warnings;

use Getopt::Long;
use DBH;

use Bio::EnsEMBL::Mapper::RangeRegistry;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Variation::DBSQL::DBAdaptor;
use ImportUtils qw(debug);
use constant MAX_LEVEL => 6;

my ($TMP_DIR, $TMP_FILE); #global variables for the tmp files and folder
my $range_registry = []; #reference to an array containing an rr for each of the possible levels (from 1-6)
#hash that, for a given individual_name, returns the individual_id in the database, if present. The last 4 samples are defined individuals in dbSNP
#with a predefined id that do not change
my %individual_id = ('Fosmid'  => '',
		     'NA11321' => '',
		     'TSC'     => '',
		     'NA10470' => '',
		     'Unknown' => '',
		     'NA07340' => 115,
		     'NA17109' => 840,
		     'NA17119' => 850
		     );
my ($chost, $cport, $cdbname, $cuser, $cpass,
    $vhost, $vport, $vdbname, $vuser, $vpass,
    $read_file);

  GetOptions('chost=s'     => \$chost,
             'cuser=s'     => \$cuser,
             'cpass=s'     => \$cpass,
             'cport=i'     => \$cport,
             'cdbname=s'   => \$cdbname,
	     'vhost=s'     => \$vhost,
             'vuser=s'     => \$vuser,
             'vpass=s'     => \$vpass,
             'vport=i'     => \$vport,
             'vdbname=s'   => \$vdbname,<commit_msg>update to set default value for NA07340, NA17109,NA17119 to different sample_id<commit_after>#!/usr/local/ensembl/bin/perl

use strict;
use warnings;

use Getopt::Long;
use DBH;

use Bio::EnsEMBL::Mapper::RangeRegistry;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Variation::DBSQL::DBAdaptor;
use ImportUtils qw(debug);
use constant MAX_LEVEL => 6;

my ($TMP_DIR, $TMP_FILE); #global variables for the tmp files and folder
my $range_registry = []; #reference to an array containing an rr for each of the possible levels (from 1-6)
#hash that, for a given individual_name, returns the individual_id in the database, if present. The last 4 samples are defined individuals in dbSNP
#with a predefined id that do not change
my %individual_id = ('Fosmid'  => '',
		     'NA11321' => '',
		     'TSC'     => '',
		     'NA10470' => '',
		     'Unknown' => '',
		     'NA07340' => 1063, ##115,
		     'NA17109' => 1703, ##840,
		     'NA17119' => 1713  ##850
		     );
my ($chost, $cport, $cdbname, $cuser, $cpass,
    $vhost, $vport, $vdbname, $vuser, $vpass,
    $read_file);

  GetOptions('chost=s'     => \$chost,
             'cuser=s'     => \$cuser,
             'cpass=s'     => \$cpass,
             'cport=i'     => \$cport,
             'cdbname=s'   => \$cdbname,
	     'vhost=s'     => \$vhost,
             'vuser=s'     => \$vuser,
             'vpass=s'     => \$vpass,
             'vport=i'     => \$vport,
             'vdbname=s'   => \$vdbname,
{'fraction_non_alphanumeric': 0.16233309908643712, 'fraction_numerical': 0.03619114546732256, 'mean_word_length': 2.563204005006258, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 41, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2467254', 'n_tokens_mistral': 1153, 'n_tokens_neox': 1022, 'n_words': 264}