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Commit a7c35a55 authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
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Backing out Dan's patches for release 59.

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misc-scripts/id_mapping/dump_by_seq_region.pl
+ 11
− 21
View file @ a7c35a55
......@@ -97,27 +97,6 @@ my $index = $conf->param('index');
my $logautobase = ($conf->param('logautobase') || 'dump_by_seq_region').
".$dbtype";
# EG - need to determine species before opening the cache and log
# determine which slice to process. To do so, read the file containing
# the slices to be processed, and take the one at position $index. This
# includes the species_id.
my $logpath = $conf->param('logpath');
my $filename = "$dbtype.dump_cache.slices.txt";
open( my $fh, '<', "$logpath/$filename" )
or throw("Unable to open $logpath/$filename for reading: $!");
my @slice_names = <$fh>;
my $slice_string = $slice_names[ $index - 1 ];
chomp($slice_string);
my ( $slice_name, $species_name, $species_id, $source_species_id ) =
split( ',', $slice_string );
close($fh);
$conf->param('basedir',path_append($conf->param('basedir'), $species_id));
$conf->param('species_id',$species_id);
$conf->param('species_name',$species_name);
# get log filehandle and print heading and parameters to logfile
my $logger = new Bio::EnsEMBL::Utils::Logger(
-LOGFILE => $conf->param('logfile'),
......@@ -139,6 +118,17 @@ my $cache = $cache_impl->new(
-CONF => $conf,
);
# determine which slice to process. to do so, read the file containing the
# slices to be processed, and take the one at position $index
my $logpath = $conf->param('logpath');
my $filename = "$dbtype.dump_cache.slices.txt";
open(my $fh, '<', "$logpath/$filename") or
throw("Unable to open $logpath/$filename for reading: $!");
my @slice_names = <$fh>;
my $slice_name = $slice_names[$index-1];
chomp($slice_name);
close($fh);
# no build the cache for this slice
$cache->build_cache_by_slice($dbtype, $slice_name);
......
misc-scripts/id_mapping/dump_cache.pl
+ 65
− 147
View file @ a7c35a55
......@@ -137,26 +137,18 @@ sub build_cache_auto {
my $cache_impl = 'Bio::EnsEMBL::IdMapping::Cache';
inject($cache_impl);
# EG - populate cache for each species in turn
$logger->debug("\nChecking number of toplevel seq_regions...\n");
my $max = 0;
my @species_ids = @{ get_species_ids("target") };
foreach my $dbtype (qw(source target)) {
# populate the cache for each species in turn
for my $species (@species_ids) {
$conf->param( 'species_id', $$species[1] );
$conf->param( 'species_name', $$species[0] );
my $cache = $cache_impl->new( -LOGGER => $logger,
-CONF => $conf, );
my $cache = $cache_impl->new(
-LOGGER => $logger,
-CONF => $conf,
);
my $num =
scalar( @{ $cache->slice_names( $dbtype, @$species ) } );
$logger->debug("\nChecking number of toplevel seq_regions...\n");
my $max = 0;
$max = $num if ( $num > $max );
$logger->debug( "$dbtype: $num.\n", 1 );
}
foreach my $dbtype (qw(source target)) {
my $num = scalar(@{ $cache->slice_names($dbtype) });
$max = $num if ($num > $max);
$logger->debug("$dbtype: $num.\n", 1);
}
my $threshold = $conf->param('build_cache_auto_threshold') || 100;
......@@ -185,144 +177,99 @@ sub build_cache_by_seq_region {
system("mkdir -p $logpath") == 0 or
$logger->error("Can't create lsf log dir $logpath: $!\n");
# EG get the list of species IDs for sources and targets
my @source_species_ids = @{ get_species_ids("source") };
my @species_ids = @{ get_species_ids("target") };
# load the cache implementation
my $cache_impl = 'Bio::EnsEMBL::IdMapping::Cache';
inject($cache_impl);
# EG store the base directory onto which the species ID will be added
my $basedir = $conf->param('basedir');
my $cache = $cache_impl->new(
-LOGGER => $logger,
-CONF => $conf,
);
# submit jobs to lsf
foreach my $dbtype (qw(source target)) {
# EG iterate over individual species for source and target
$logger->info("\n".ucfirst($dbtype)." db...\n", 0, 'stamped');
# determine which slices need to be done
my $filename = "$dbtype.dump_cache.slices.txt";
open( my $fh, '>', "$logpath/$filename" )
or throw("Unable to open $logpath/$filename for writing: $!");
open(my $fh, '>', "$logpath/$filename") or
throw("Unable to open $logpath/$filename for writing: $!");
my $num_jobs = 0;
for my $species (@species_ids) {
# EG set config based on species ID in turn
$conf->param( 'basedir', path_append( $basedir, $$species[1] ) );
$conf->param( 'species_id', $$species[1] );
$conf->param( 'species_name', $$species[0] );
# EG load cache for current species ID
my $cache = $cache_impl->new( -LOGGER => $logger,
-CONF => $conf, );
foreach my $slice_name (
@{ $cache->slice_names( $dbtype, @$species ) } )
{
my $type = "$dbtype.$slice_name";
my $src_species_id;
for my $src_id (@source_species_ids) {
if ( $$species[1] == $$src_id[1] ) {
$src_species_id = $$src_id[1];
last;
}
}
$logger->info( "\n" . ucfirst($dbtype) . " db...\n",
0, 'stamped' );
my $type = "$dbtype.$slice_name";
unless ( $cache->cache_file_exists($type) ) {
print $fh "$slice_name,$$species[0],$$species[1],"
. $src_species_id . "\n";
$num_jobs++;
}
}
unless ($num_jobs) {
$logger->info("All cache files for $dbtype exist.\n");
next;
foreach my $slice_name (@{ $cache->slice_names($dbtype) }) {
my $type = "$dbtype.$slice_name";
unless ($cache->cache_file_exists($type)) {
print $fh "$slice_name\n";
$num_jobs++;
}
}
} ## end for my $species (@species_ids)
close($fh);
# EG reset original basedir
$conf->param( 'basedir', $basedir );
unless ($num_jobs) {
$logger->info("All cache files for $dbtype exist.\n");
next;
}
# build lsf command
my $lsf_name = 'dump_by_seq_region_' . time;
my $lsf_name = 'dump_by_seq_region_'.time;
my $concurrent = $conf->param('build_cache_concurrent_jobs') || 200;
my $options =
$conf->create_commandline_options(
logauto => 1,
logautobase => "dump_by_seq_region",
interactive => 0,
is_component => 1,
dbtype => $dbtype,
cache_impl => $cache_impl, );
# EG invoke perl with correct path rather than relying on shebang
my $cmd = 'perl dump_by_seq_region.pl '
. qq{$options --index \$LSB_JOBINDEX};
my $pipe =
'|bsub '
. $conf->param('lsf_opt_run')
. qq{ -J '$lsf_name\[1-$num_jobs\]\%$concurrent' }
. qq{-o $logpath/dump_by_seq_region.$dbtype.\%I.out }
. qq{-e $logpath/dump_by_seq_region.$dbtype.\%I.err }
. $conf->param('lsf_opt_dump_cache');
my $options = $conf->create_commandline_options(
logauto => 1,
logautobase => "dump_by_seq_region",
interactive => 0,
is_component => 1,
dbtype => $dbtype,
cache_impl => $cache_impl,
);
# run lsf job array
$logger->info("\nSubmitting $num_jobs jobs to lsf.\n");
my $cmd = qq{./dump_by_seq_region.pl $options --index \$LSB_JOBINDEX};
if ( $num_jobs > 0 ) {
$logger->debug("$cmd\n\n");
$logger->debug("$pipe\n\n");
my $pipe = qq{|bsub -J$lsf_name\[1-$num_jobs\]\%$concurrent } .
qq{-o $logpath/dump_by_seq_region.$dbtype.\%I.out } .
qq{-e $logpath/dump_by_seq_region.$dbtype.\%I.err } .
$conf->param('lsf_opt_dump_cache');
local *BSUB;
open BSUB, $pipe
or $logger->error("Could not open open pipe to bsub: $!\n");
# run lsf job array
$logger->info("\nSubmitting $num_jobs jobs to lsf.\n");
$logger->debug("$cmd\n\n");
print BSUB $cmd;
$logger->error("Error submitting jobs: $!\n")
unless ( $? == 0 );
close BSUB;
local *BSUB;
open BSUB, $pipe or
$logger->error("Could not open open pipe to bsub: $!\n");
# submit dependent job to monitor finishing of jobs
$logger->info( "Waiting for jobs to finish...\n", 0, 'stamped' );
print BSUB $cmd;
$logger->error("Error submitting jobs: $!\n")
unless ($? == 0);
close BSUB;
my $dependent_job =
qq{bsub -K -w "ended($lsf_name)" }
. $conf->param('lsf_opt_run_small')
. qq{ -o $logpath/dump_cache.$dbtype.depend.out /bin/true};
# submit dependent job to monitor finishing of jobs
$logger->info("Waiting for jobs to finish...\n", 0, 'stamped');
system($dependent_job) == 0
or $logger->error("Error submitting dependent job: $!\n");
my $dependent_job = qq{bsub -K -w "ended($lsf_name)" -q small } .
qq{-o $logpath/dump_cache.$dbtype.depend.out /bin/true};
$logger->info( "All jobs finished.\n", 0, 'stamped' );
system($dependent_job) == 0 or
$logger->error("Error submitting dependent job: $!\n");
sleep(5);
} ## end if ( $num_jobs > 0 )
$logger->info("All jobs finished.\n", 0, 'stamped');
# check for lsf errors
sleep(5);
my $err;
foreach my $i ( 1 .. $num_jobs ) {
if ( !-e "$logpath/dump_by_seq_region.$dbtype.$i.success" ) {
$err++;
}
foreach my $i (1..$num_jobs) {
$err++ unless (-e "$logpath/dump_by_seq_region.$dbtype.$i.success");
}
if ( $err > 0 ) {
$logger->error( "At least one of your jobs failed.\n"
. "Please check the logfiles at $logpath for errors.\n" );
if ($err) {
$logger->error("At least one of your jobs failed.\nPlease check the logfiles at $logpath for errors.\n");
return 1;
}
} ## end foreach my $dbtype (qw(source target))
}
return 0;
}
......@@ -357,32 +304,3 @@ sub build_cache_all {
}
# EG new method for getting species IDs
sub get_species_ids {
my ($prefix) = @_;
my @speciesIds;
my $dsn =
"DBI:mysql:database="
. $conf->param("${prefix}dbname")
. ";host="
. $conf->param("${prefix}host")
. ";port="
. $conf->param("${prefix}port");
my $ensemblCoreDbh = DBI->connect( $dsn,
$conf->param("${prefix}user"),
$conf->param("${prefix}pass") )
|| die "Cannot connect to server: $DBI::errstr\n";
my $query = "SELECT DISTINCT meta_value, species_id
FROM meta WHERE meta_key = 'species.production_name'";
my $psmt = $ensemblCoreDbh->prepare($query);
$psmt->execute();
while ( my (@results) = $psmt->fetchrow() ) {
push @speciesIds, [ $results[0], $results[1] ];
}
return \@speciesIds;
} ## end sub get_species_ids
misc-scripts/id_mapping/id_mapping.pl
+ 74
− 242
View file @ a7c35a55
......@@ -56,8 +56,7 @@ no warnings 'uninitialized';
use FindBin qw($Bin);
use Bio::EnsEMBL::Utils::ConfParser;
use Bio::EnsEMBL::Utils::Logger;
use Bio::EnsEMBL::Utils::Exception qw(throw);
use Bio::EnsEMBL::Utils::ScriptUtils qw(path_append inject);
use Bio::EnsEMBL::Utils::ScriptUtils qw(path_append);
use Bio::EnsEMBL::IdMapping::Cache;
use Bio::EnsEMBL::IdMapping::ExonScoreBuilder;
use Bio::EnsEMBL::IdMapping::TranscriptScoreBuilder;
......@@ -78,38 +77,26 @@ my $conf = new Bio::EnsEMBL::Utils::ConfParser(
);
$conf->parse_options(
'mode=s' => 0,
'basedir|basedir=s' => 1,
'chromosomes|chr=s@' => 0,
'region=s' => 0,
'biotypes=s@' => 0,
'min_exon_length|minexonlength=i' => 0,
'exonerate_path|exoneratepath=s' => 1,
'exonerate_threshold|exoneratethreshold=f' => 0,
'exonerate_jobs|exoneratejobs=i' => 0,
'mode=s' => 0,
'basedir|basedir=s' => 1,
'chromosomes|chr=s@' => 0,
'region=s' => 0,
'biotypes=s@' => 0,
'min_exon_length|minexonlength=i' => 0,
'exonerate_path|exoneratepath=s' => 1,
'exonerate_threshold|exoneratethreshold=f' => 0,
'exonerate_jobs|exoneratejobs=i' => 0,
'exonerate_bytes_per_job|exoneratebytesperjob=f' => 0,
'exonerate_extra_params|exonerateextraparams=s' => 0,
'plugin_internal_id_mappers_gene=s@' => 0,
'plugin_internal_id_mappers_transcript=s@' => 0,
'plugin_internal_id_mappers_exon=s@' => 0,
'mapping_types=s@' => 1,
'plugin_stable_id_generator=s' => 0,
'upload_events|uploadevents=s' => 0,
'upload_stable_ids|uploadstableids=s' => 0,
'upload_archive|uploadarchive=s' => 0,
# EG allow additional configs to be set on command line
'sourcedbname=s' => 1,
'sourcehost=s' => 1,
'sourceuser=s' => 1,
'sourcepass=s' => 0,
'sourceport=i' => 1,
'targetdbname=s' => 1,
'targethost=s' => 1,
'targetuser=s' => 1,
'targetpass=s' => 0,
'targetport=i' => 1,
'species_id' => 0,
'species_name' => 0 );
'exonerate_extra_params|exonerateextraparams=s' => 0,
'plugin_internal_id_mappers_gene=s@' => 0,
'plugin_internal_id_mappers_transcript=s@' => 0,
'plugin_internal_id_mappers_exon=s@' => 0,
'mapping_types=s@' => 1,
'plugin_stable_id_generator=s' => 0,
'upload_events|uploadevents=s' => 0,
'upload_stable_ids|uploadstableids=s' => 0,
'upload_archive|uploadarchive=s' => 0,
);
# set default logpath
unless ($conf->param('logpath')) {
......@@ -144,109 +131,35 @@ my $transcript_mappings;
my $gene_mappings;
my $translation_mappings;
# EG mapping code reworked to iterate over different species
# loading cache from file
my $cache = Bio::EnsEMBL::IdMapping::Cache->new(
-LOGGER => $logger,
-CONF => $conf,
-LOAD_INSTANCE => 1,
);
# get a stable ID mapper
my $stable_id_mapper = Bio::EnsEMBL::IdMapping::StableIdMapper->new(
-LOGGER => $logger,
-CONF => $conf,
-CACHE => $cache
);
# find out which entities we want to map
my %mapping_types = ();
foreach my $type ( $conf->param('mapping_types') ) {
foreach my $type ($conf->param('mapping_types')) {
$mapping_types{$type} = 1;
}
# EG get list of species
my @species_ids = @{ get_species_ids( "target", $conf ) };
my $basedir = $conf->param('basedir');
# EG create placeholder cache based on the first species to allow us to
# create a stable ID generator to reuse for all species
my $stable_id_mapper;
my $s = $species_ids[0];
$conf->param( 'basedir', path_append( $basedir, $$s[1] ) );
$conf->param( 'species_id', $$s[1] );
$conf->param( 'species_name', $$s[0] );
# loading cache from file
my $cache = Bio::EnsEMBL::IdMapping::Cache->new(
-LOGGER => $logger,
-CONF => $conf,
-LOAD_INSTANCE => 1,
-SPECIES_ID => $$s[1], # EG
-SPECIES_NAME => $$s[0] # EG
);
my $type_count_sql = { gene => 'select count(*) '
. 'from gene_stable_id '
. 'join gene using (gene_id) '
. 'join seq_region using (seq_region_id) '
. 'join coord_system using (coord_system_id) '
. 'where species_id=?',
transcript => 'select count(*) '
. 'from transcript_stable_id '
. 'join transcript using (transcript_id) '
. 'join seq_region using (seq_region_id) '
. 'join coord_system using (coord_system_id) '
. 'where species_id=?',
exon => 'select count(*) '
. 'from exon_stable_id '
. 'join exon using (exon_id) '
. 'join seq_region using (seq_region_id) '
. 'join coord_system using (coord_system_id) '
. 'where species_id=?',
translation => 'select count(*) '
. 'from translation_stable_id '
. 'join translation using (translation_id) '
. 'join transcript using (transcript_id) '
. 'join seq_region using (seq_region_id) '
. 'join coord_system using (coord_system_id) '
. 'where species_id=?' };
# eg get the stable id generator and inject the cache into it
my $stable_id_generator = $conf->param('plugin_stable_id_generator')
|| 'Bio::EnsEMBL::IdMapping::StableIdGenerator::EnsemblGeneric';
inject($stable_id_generator);
# create a new stableidgenerator object
my $generator_instance =
$stable_id_generator->new( -logger => $logger,
-conf => $conf,
-cache => $cache );
# EG iterate over species
for my $species (@species_ids) {
# EG create a new cache for the current species
print( "Handling species " . $$species[0] . "/" . $$species[1],
"\n" );
$conf->param( 'basedir', path_append( $basedir, $$species[1] ) );
$conf->param( 'species_id', $$species[1] );
$conf->param( 'species_name', $$species[0] );
$cache =
Bio::EnsEMBL::IdMapping::Cache->new( -LOGGER => $logger,
-CONF => $conf,
-LOAD_INSTANCE => 1 );
# get a stable ID mapper
$stable_id_mapper =
Bio::EnsEMBL::IdMapping::StableIdMapper->new( -LOGGER => $logger,
-CONF => $conf,
-CACHE => $cache );
# EG replace the genny cache with the species specific one
$generator_instance->cache($cache);
$stable_id_mapper->stable_id_generator($generator_instance);
##? # find out which entities we want to map
##? my %mapping_types = ();
##? foreach my $type ( $conf->param('mapping_types') ) {
##? $mapping_types{$type} = 1;
##? }
# run in requested mode
my $mode = $conf->param('mode') || 'normal';
if ( $mode eq 'mapping' ) { $mode = 'normal' }
my $run = "run_$mode";
no strict 'refs';
&$run;
} ## end for my $species (@species_ids)
# run in requested mode
my $mode = $conf->param('mode') || 'normal';
if ( $mode eq 'mapping' ) { $mode = 'normal' }
my $run = "run_$mode";
no strict 'refs';
&$run;
# finish logfile
......@@ -474,73 +387,49 @@ sub archive {
sub upload_mapping_session_and_events {
if ( $conf->is_true('upload_events') and !$conf->param('dry_run') ) {
$logger->info(
"Uploading mapping_session and stable_id_event tables...\n");
if ($conf->is_true('upload_events') and ! $conf->param('dry_run')) {
$logger->info("Uploading mapping_session and stable_id_event tables...\n");
my $i = 0;
my $j = 0;
$logger->info( "mapping_session...\n", 1 );
$i +=
$stable_id_mapper->upload_file_into_table( 'target',
'mapping_session', 'mapping_session.txt',
$conf->param('species_id') > 1 ? 1 : 0 );
$logger->info( "$i\n", 1 );
$logger->info( "stable_id_event...\n", 1 );
$j += $stable_id_mapper->upload_file_into_table( 'target',
'stable_id_event', 'stable_id_event_existing.txt' );
$j += $stable_id_mapper->upload_file_into_table( 'target',
'stable_id_event', 'stable_id_event_new.txt', 1 );
$j += $stable_id_mapper->upload_file_into_table( 'target',
'stable_id_event', 'stable_id_event_similarity.txt', 1 );
$logger->info( "$j\n", 1 );
$logger->info("mapping_session...\n", 1);
$i += $stable_id_mapper->upload_file_into_table('target', 'mapping_session',
'mapping_session.txt');
$logger->info("$i\n", 1);
$logger->info("stable_id_event...\n", 1);
$j += $stable_id_mapper->upload_file_into_table('target', 'stable_id_event',
'stable_id_event_existing.txt');
$j += $stable_id_mapper->upload_file_into_table('target', 'stable_id_event',
'stable_id_event_new.txt', 1);
$j += $stable_id_mapper->upload_file_into_table('target', 'stable_id_event',
'stable_id_event_similarity.txt', 1);
$logger->info("$j\n", 1);
$logger->info("Done.\n\n");
} else {
$logger->info(
"Stable ID event and mapping session tables not uploaded.\n\n");
$logger->info("Stable ID event and mapping session tables not uploaded.\n\n");
}
} ## end sub upload_mapping_session_and_events
}
sub upload_stable_ids {
if ( $conf->is_true('upload_stable_ids')
&& !$conf->param('dry_run') )
{
my $species_id = $conf->param('species_id');
if ($conf->is_true('upload_stable_ids') and ! $conf->param('dry_run')) {
$logger->info("Uploading stable ID tables...\n");
foreach my $t ( $conf->param('mapping_types') ) {
$logger->info( "${t}_stable_id...\n", 1 );
# EG check if empty for species
my $cnt = get_stable_id_count( $t, 'target', $species_id );
if ( $cnt > 0 ) {
$logger->warning( "Existing stable IDs found "
. "for $t for species ID $species_id "
. "- not uploading",
1 );
$logger->info( "Data not uploaded!\n", 1 );
} else {
my $i = $stable_id_mapper->upload_file_into_table( 'target',
"${t}_stable_id", "${t}_stable_id.txt", 1 );
$logger->info( "$i\n", 1 );
}
foreach my $t ($conf->param('mapping_types')) {
$logger->info("${t}_stable_id...\n", 1);
my $i = $stable_id_mapper->upload_file_into_table('target',
"${t}_stable_id", "${t}_stable_id.txt");
$logger->info("$i\n", 1);
}
$logger->info("Done.\n\n");
} else {
$logger->info("Stable ID tables not uploaded.\n\n");
}
......@@ -650,61 +539,4 @@ sub log_cache_stats {
}
}
sub get_stable_id_count {
my ( $type, $dbtype, $species_id ) = @_;
# EG new subroutine for finding if stable ID table has entries for
# this species already
my $dba = $cache->get_DBAdaptor($dbtype);
my $dbh = $dba->dbc->db_handle;
# check table is empty
my $sql = $type_count_sql->{$type};
if ( !defined($sql) ) {
throw("Cannot count stable ids of type $type");
}
my $sth = $dbh->prepare($sql);
$sth->execute($species_id);
my ($c) = $sth->fetchrow_array;
$sth->finish;
return $c;
}
sub get_species_ids {
my ( $prefix, $conf ) = @_;
# EG additional subroutine for determining which species IDs are
# present
my @speciesIds;
my $dsn =
"DBI:mysql:database="
. $conf->param("${prefix}dbname")
. ";host="
. $conf->param("${prefix}host")
. ";port="
. $conf->param("${prefix}port");
my $ensemblCoreDbh = DBI->connect( $dsn,
$conf->param("${prefix}user"),
$conf->param("${prefix}pass") )
|| die "Cannot connect to server: $DBI::errstr\n";
my $query = "SELECT DISTINCT meta_value, species_id
FROM meta WHERE meta_key = 'species.production_name'";
my $psmt = $ensemblCoreDbh->prepare($query);
$psmt->execute();
while ( my (@results) = $psmt->fetchrow() ) {
push @speciesIds, [ $results[0], $results[1] ];
}
return \@speciesIds;
} ## end sub get_species_ids
misc-scripts/id_mapping/myRun.ksh
+ 1
− 1
View file @ a7c35a55
......@@ -52,6 +52,6 @@ if [[ ${conf#/} == ${conf} ]]; then
exit
fi
./run.pl --lsf --conf=${conf} --mode=${mode} --logauto
./run.pl --lsf --conf=${conf} --logauto --mode=${mode}
# $Id$
misc-scripts/id_mapping/synteny_rescore.pl
+ 6
− 17
View file @ a7c35a55
......@@ -67,23 +67,12 @@ my $conf = new Bio::EnsEMBL::Utils::ConfParser(
-DEFAULT_CONF => "$Bin/default.conf"
);
$conf->parse_options( 'basedir|basedir=s' => 1,
'index|i=n' => 1,
'chromosomes|chr=s@' => 0,
'region=s' => 0,
'species_id=i' => 1,
'species_name=s' => 1,
'sourcedbname=s' => 1,
'sourcehost=s' => 1,
'sourceuser=s' => 1,
'sourcepass=s' => 0,
'sourceport=i' => 1,
'targetdbname=s' => 1,
'targethost=s' => 1,
'targetuser=s' => 1,
'targetpass=s' => 0,
'targetport=i' => 1 );
$conf->parse_options(
'basedir|basedir=s' => 1,
'index|i=n' => 1,
'chromosomes|chr=s@' => 0,
'region=s' => 0,
);
# append job index to logfile name
my $index = $conf->param('index');
......
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