Mercurial > repos > mahtabm > ensembl
diff variant_effect_predictor/Bio/EnsEMBL/AssemblyMapper.pm @ 0:1f6dce3d34e0
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| author | mahtabm |
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| date | Thu, 11 Apr 2013 02:01:53 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/variant_effect_predictor/Bio/EnsEMBL/AssemblyMapper.pm Thu Apr 11 02:01:53 2013 -0400 @@ -0,0 +1,880 @@ +=head1 LICENSE + + Copyright (c) 1999-2012 The European Bioinformatics Institute and + Genome Research Limited. All rights reserved. + + This software is distributed under a modified Apache license. + For license details, please see + + http://www.ensembl.org/info/about/code_licence.html + +=head1 CONTACT + + Please email comments or questions to the public Ensembl + developers list at <dev@ensembl.org>. + + Questions may also be sent to the Ensembl help desk at + <helpdesk@ensembl.org>. + +=cut + +=head1 NAME + +Bio::EnsEMBL::AssemblyMapper - +Handles mapping between two coordinate systems using the information +stored in the assembly table. + +=head1 SYNOPSIS + + $db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(...); + $asma = $db->get_AssemblyMapperAdaptor(); + $csa = $db->get_CoordSystemAdaptor(); + + my $chr_cs = $cs_adaptor->fetch_by_name( 'chromosome', 'NCBI33' ); + my $ctg_cs = $cs_adaptor->fetch_by_name('contig'); + + $asm_mapper = $map_adaptor->fetch_by_CoordSystems( $cs1, $cs2 ); + + # Map to contig coordinate system from chromosomal. + @ctg_coords = + $asm_mapper->map( 'X', 1_000_000, 2_000_000, 1, $chr_cs ); + + # Map to chromosome coordinate system from contig. + @chr_coords = + $asm_mapper->map( 'AL30421.1.200.92341', 100, 10000, -1, + $ctg_cs ); + + # List contig names for a region of chromsome. + @ctg_ids = $asm_mapper->list_ids( '13', 1_000_000, 1, $chr_cs ); + + # List chromosome names for a contig region. + @chr_ids = + $asm_mapper->list_ids( 'AL30421.1.200.92341', 1, 1000, -1, + $ctg_cs ); + +=head1 DESCRIPTION + +The AssemblyMapper is a database aware mapper which faciliates +conversion of coordinates between any two coordinate systems with an +relationship explicitly defined in the assembly table. In the future +it may be possible to perform multiple step (implicit) mapping between +coordinate systems. + +It is implemented using the Bio::EnsEMBL::Mapper object, which is a +generic mapper object between disjoint coordinate systems. + +=head1 METHODS + +=cut + + +package Bio::EnsEMBL::AssemblyMapper; + +use strict; +use warnings; + +use Bio::EnsEMBL::Mapper; +use Bio::EnsEMBL::Utils::Exception qw(throw deprecate); +use Scalar::Util qw(weaken); + +my $ASSEMBLED = 'assembled'; +my $COMPONENT = 'component'; + +my $DEFAULT_MAX_PAIR_COUNT = 1000; + + +=head2 new + + Arg [1] : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor + Arg [2] : Bio::EnsEMBL::CoordSystem $asm_cs + Arg [3] : Bio::EnsEMBL::CoordSystem $cmp_cs + Example : Should use AssemblyMapperAdaptor->fetch_by_CoordSystems() + Description: Creates a new AssemblyMapper + Returntype : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor + Exceptions : Throws if multiple coord_systems are provided + Caller : AssemblyMapperAdaptor + Status : Stable + +=cut + +sub new { + my ( $proto, $adaptor, @coord_systems ) = @_; + + my $class = ref($proto) || $proto; + + my $self = bless( {}, $class ); + + $self->adaptor($adaptor); + + $adaptor->cache_seq_ids_with_mult_assemblys(); + + if ( @coord_systems != 2 ) { + throw( 'Can only map between two coordinate systems. ' + . scalar(@coord_systems) + . ' were provided' ); + } + + # Set the component and assembled coordinate systems + $self->{'asm_cs'} = $coord_systems[0]; + $self->{'cmp_cs'} = $coord_systems[1]; + + # We load the mapper calling the 'ASSEMBLED' the 'from' coord system + # and the 'COMPONENT' the 'to' coord system. + + $self->{'mapper'} = Bio::EnsEMBL::Mapper->new( $ASSEMBLED, $COMPONENT, + $coord_systems[0], $coord_systems[1] ); + + $self->{'max_pair_count'} = $DEFAULT_MAX_PAIR_COUNT; + + return $self; +} ## end sub new + +=head2 max_pair_count + + Arg [1] : (optional) int $max_pair_count + Example : $mapper->max_pair_count(100000) + Description: Getter/Setter for the number of mapping pairs allowed + in the internal cache. This can be used to override + the default value (1000) to tune the performance and + memory usage for certain scenarios. Higher value + means bigger cache, more memory used. + Return type: int + Exceptions : None + Caller : General + Status : Stable + +=cut + +sub max_pair_count { + my ( $self, $value ) = @_; + + if ( defined($value) ) { + $self->{'max_pair_count'} = $value; + } + + return $self->{'max_pair_count'}; +} + +=head2 register_all + + Arg [1] : None + Example : $mapper->max_pair_count(10e6); + $mapper->register_all(); + Description: Pre-registers all assembly information in this + mapper. The cache size should be set to a + sufficiently large value so that all of the + information can be stored. This method is useful + when *a lot* of mapping will be done in regions + which are distributed around the genome. After + registration the mapper will consume a lot of memory + but will not have to perform any SQL and will be + faster. + Return type: None + Exceptions : None + Caller : Specialised programs doing a lot of mapping. + Status : Stable + +=cut + +sub register_all { + my ($self) = @_; + + $self->adaptor()->register_all($self); +} + +=head2 map + + Arg [1] : string $frm_seq_region + The name of the sequence region to transform FROM. + Arg [2] : int $frm_start + The start of the region to transform FROM. + Arg [3] : int $frm_end + The end of the region to transform FROM. + Arg [4] : int $strand + The strand of the region to transform FROM. + Arg [5] : Bio::EnsEMBL::CoordSystem + The coordinate system to transform FROM + Example : @coords = + $asm_mapper->map( 'X', 1_000_000, 2_000_000, 1, + $chr_cs ); + Description: Transforms coordinates from one coordinate system to + another. + Return type: List of Bio::EnsEMBL::Mapper::Coordinate and/or + Bio::EnsEMBL::Mapper:Gap objects. + Exceptions : Throws if if the specified TO coordinat system is not + one of the coordinate systems associated with this + assembly mapper. + Caller : General + Status : Stable + +=cut + +sub map { + throw('Incorrect number of arguments.') if (!( @_ >= 6)); + + my ( $self, $frm_seq_region_name, $frm_start, $frm_end, $frm_strand, + $frm_cs, $to_slice ) + = @_; + + my $mapper = $self->{'mapper'}; + my $asm_cs = $self->{'asm_cs'}; + my $cmp_cs = $self->{'cmp_cs'}; + my $adaptor = $self->{'adaptor'}; + my $frm; + + + my $seq_region_id = + $self->adaptor() + ->seq_regions_to_ids( $frm_cs, [$frm_seq_region_name] )->[0]; + + # Speed critical section: + # Try to do simple pointer equality comparisons of the coord system + # objects first since this is likely to work most of the time and is + # much faster than a function call. + + if ( $frm_cs == $cmp_cs + || ( $frm_cs != $asm_cs && $frm_cs->equals($cmp_cs) ) ) + { + if ( !$self->{'cmp_register'}->{$seq_region_id} ) { + $adaptor->register_component( $self, $seq_region_id ); + } + $frm = $COMPONENT; + + } elsif ( $frm_cs == $asm_cs || $frm_cs->equals($asm_cs) ) { + + # This can be probably be sped up some by only calling registered + # assembled if needed. + $adaptor->register_assembled( $self, $seq_region_id, $frm_start, + $frm_end ); + $frm = $ASSEMBLED; + + } else { + + throw( + sprintf( "Coordinate system %s %s is neither the assembled " + . "nor the component coordinate system " + . "of this AssemblyMapper", + $frm_cs->name(), $frm_cs->version() ) ); + + } + + return + $mapper->map_coordinates( $seq_region_id, $frm_start, $frm_end, + $frm_strand, $frm ); +} ## end sub map + + +=head2 flush + + Args : None + Example : None + Description: Remove all cached items from this AssemblyMapper. + Return type: None + Exceptions : None + Caller : AssemblyMapperAdaptor + Status : Stable + +=cut + +sub flush { + my ($self) = @_; + + $self->{'mapper'}->flush(); + $self->{'cmp_register'} = {}; + $self->{'asm_register'} = {}; +} + +=head2 size + + Args : None + Example : $num_of_pairs = $mapper->size(); + Description: Returns the number of pairs currently stored. + Return type: int + Exceptions : None + Caller : General + Status : Stable + +=cut + +sub size { + my ($self) = @_; + + return $self->{'mapper'}->{'pair_count'}; +} + +=head2 fastmap + + Arg [1] : string $frm_seq_region + The name of the sequence region to transform FROM. + Arg [2] : int $frm_start + The start of the region to transform FROM. + Arg [3] : int $frm_end + The end of the region to transform FROM. + Arg [4] : int $strand + The strand of the region to transform FROM. + Arg [5] : Bio::EnsEMBL::CoordSystem + The coordinate system to transform FROM. + Example : @coords = + $asm_mapper->map( 'X', 1_000_000, 2_000_000, 1, + $chr_cs ); + Description: Transforms coordinates from one coordinate system to + another. + Return type: List of Bio::EnsEMBL::Mapper::Coordinate and/or + Bio::EnsEMBL::Mapper:Gap objects. + Exceptions : Throws if the specified TO coordinat system is not + one of the coordinate systems associated with this + assembly mapper. + Caller : General + Status : Stable + +=cut + +sub fastmap { + if ( @_ != 6 ) { + throw('Incorrect number of arguments.'); + } + + my ( $self, $frm_seq_region_name, $frm_start, $frm_end, $frm_strand, + $frm_cs ) + = @_; + + my $mapper = $self->{'mapper'}; + my $asm_cs = $self->{'asm_cs'}; + my $cmp_cs = $self->{'cmp_cs'}; + my $adaptor = $self->adaptor(); + my $frm; + + my @tmp; + push @tmp, $frm_seq_region_name; + + my $seq_region_id = + $self->adaptor()->seq_regions_to_ids( $frm_cs, \@tmp )->[0]; + + # Speed critical section: + # Try to do simple pointer equality comparisons of the coord system + # objects first since this is likely to work most of the time and is + # much faster than a function call. + + if ( $frm_cs == $cmp_cs + || ( $frm_cs != $asm_cs && $frm_cs->equals($cmp_cs) ) ) + { + + if ( !$self->{'cmp_register'}->{$seq_region_id} ) { + $adaptor->register_component( $self, $seq_region_id ); + } + $frm = $COMPONENT; + + } elsif ( $frm_cs == $asm_cs || $frm_cs->equals($asm_cs) ) { + + # This can be probably be sped up some by only calling registered + # assembled if needed + $adaptor->register_assembled( $self, $seq_region_id, $frm_start, + $frm_end ); + $frm = $ASSEMBLED; + + } else { + + throw( + sprintf( "Coordinate system %s %s is neither the assembled " + . "nor the component coordinate system " + . "of this AssemblyMapper", + $frm_cs->name(), $frm_cs->version() ) ); + + } + + return + $mapper->fastmap( $seq_region_id, $frm_start, $frm_end, $frm_strand, + $frm ); +} ## end sub fastmap + +=head2 list_ids + + Arg [1] : string $frm_seq_region + The name of the sequence region of interest. + Arg [2] : int $frm_start + The start of the region of interest. + Arg [3] : int $frm_end + The end of the region to transform of interest. + Arg [5] : Bio::EnsEMBL::CoordSystem $frm_cs + The coordinate system to obtain overlapping IDs of. + Example : foreach my $id ( + $asm_mapper->list_ids( 'X', 1, 1000, $ctg_cs ) ) + { ... } + Description: Retrieves a list of overlapping seq_region names of + another coordinate system. This is the same as the + list_ids method but uses seq_region names rather + internal IDs. + Return type: List of strings. + Exceptions : None + Caller : General + Status : Stable + +=cut + +sub list_ids { + if ( @_ != 5 ) { + throw('Incorrect number of arguments.'); + } + + my ( $self, $frm_seq_region_name, $frm_start, $frm_end, $frm_cs ) = + @_; + + my @tmp = ($frm_seq_region_name); + + my $seq_region_id = + $self->adaptor()->seq_regions_to_ids( $frm_cs, \@tmp )->[0]; + + if ( $frm_cs->equals( $self->component_CoordSystem() ) ) { + + if ( !$self->have_registered_component($seq_region_id) ) { + $self->adaptor->register_component( $self, $seq_region_id ); + } + + # Pull out the 'from' identifiers of the mapper pairs. The we + # loaded the assembled side as the 'from' side in the constructor. + + return + map ( { $_->from()->id() } + $self->mapper()->list_pairs( + $seq_region_id, $frm_start, $frm_end, $COMPONENT + ) ); + + } elsif ( $frm_cs->equals( $self->assembled_CoordSystem() ) ) { + + $self->adaptor->register_assembled( $self, $seq_region_id, + $frm_start, $frm_end ); + + # Pull out the 'to' identifiers of the mapper pairs we loaded the + # component side as the 'to' coord system in the constructor. + + return + map ( { $_->to->id() } + $self->mapper()->list_pairs( + $seq_region_id, $frm_start, $frm_end, $ASSEMBLED + ) ); + + } else { + + throw( + sprintf( "Coordinate system %s %s is neither the assembled " + . "nor the component coordinate system " + . "of this AssemblyMapper", + $frm_cs->name(), $frm_cs->version() ) ); + + } +} ## end sub list_ids + +#sub list_seq_regions { +# throw('Incorrect number of arguments.') if(@_ != 5); +# my($self, $frm_seq_region_name, $frm_start, $frm_end, $frm_cs) = @_; + +# if($frm_cs->equals($self->component_CoordSystem())) { + +# if(!$self->have_registered_component($seq_region_id)) { +# $self->adaptor->register_component($self,$seq_region_id); +# } + +# #pull out the 'from' identifiers of the mapper pairs. The +# #we loaded the assembled side as the 'from' side in the constructor +# return +# map {$_->from()->id()} +# $self->mapper()->list_pairs($seq_region_id, $frm_start, +# $frm_end, $COMPONENT); + +# } elsif($frm_cs->equals($self->assembled_CoordSystem())) { + +# $self->adaptor->register_assembled($self, +# $frm_seq_region,$frm_start,$frm_end); + +# #pull out the 'to' identifiers of the mapper pairs +# #we loaded the component side as the 'to' coord system in the constructor +# return +# map {$_->to->id()} +# $self->mapper()->list_pairs($frm_seq_region, $frm_start, +# $frm_end, $ASSEMBLED); +# } else { +# throw("Coordinate system " . $frm_cs->name . " " . $frm_cs->version . +# " is neither the assembled nor the component coordinate system " . +# " of this AssemblyMapper"); +# } +#} + + +=head2 list_seq_regions + + Arg [1] : string $frm_seq_region + The name of the sequence region of interest. + Arg [2] : int $frm_start + The start of the region of interest. + Arg [3] : int $frm_end + The end of the region to transform of interest. + Arg [5] : Bio::EnsEMBL::CoordSystem $frm_cs + The coordinate system to obtain overlapping IDs of. + Example : foreach my $id ( + $asm_mapper->list_seq_regions( + 'X', 1, 1000, $chr_cs + ) ) { ... } + Description: Retrieves a list of overlapping seq_region internal + identifiers of another coordinate system. This is + the same as the list_seq_regions method but uses + internal identfiers rather than seq_region strings. + Return type: List of ints. + Exceptions : None + Caller : General + Status : Stable + +=cut + +sub list_seq_regions { + if ( @_ != 5 ) { + throw('Incorrect number of arguments.'); + } + + my ( $self, $frm_seq_region, $frm_start, $frm_end, $frm_cs ) = @_; + + # Retrieve the seq_region names. + + my @seq_ids = + $self->list_ids( $frm_seq_region, $frm_start, $frm_end, $frm_cs ); + + # The seq_regions are from the 'to' coordinate system not the from + # coordinate system we used to obtain them. + + my $to_cs; + if ( $frm_cs->equals( $self->assembled_CoordSystem() ) ) { + $to_cs = $self->component_CoordSystem(); + } else { + $to_cs = $self->assembled_CoordSystem(); + } + + # Convert them to IDs. + return @{ $self->adaptor()->seq_ids_to_regions( \@seq_ids ) }; +} + +#sub list_ids { +# throw('Incorrect number of arguments.') if(@_ != 5); +# my($self, $frm_seq_region, $frm_start, $frm_end, $frm_cs) = @_; + +# #retrieve the seq_region names +# my @seq_regs = +# $self->list_seq_regions($frm_seq_region,$frm_start,$frm_end,$frm_cs); + +# #The seq_regions are from the 'to' coordinate system not the +# #from coordinate system we used to obtain them +# my $to_cs; +# if($frm_cs->equals($self->assembled_CoordSystem())) { +# $to_cs = $self->component_CoordSystem(); +# } else { +# $to_cs = $self->assembled_CoordSystem(); +# } + +# #convert them to ids +# return @{$self->adaptor()->seq_regions_to_ids($to_cs, \@seq_regs)}; +#} + +=head2 have_registered_component + + Arg [1] : string $cmp_seq_region + The name of the sequence region to check for + registration. + Example : if ( $asm_mapper->have_registered_component('AL240214.1') ) {} + Description: Returns true if a given component region has + been registered with this assembly mapper. This + should only be called by this class or the + AssemblyMapperAdaptor. In other words, do not use + this method unless you really know what you are + doing. + Return type: Boolean (0 or 1) + Exceptions : Throws on incorrect arguments. + Caller : Internal, AssemblyMapperAdaptor + Status : Stable + +=cut + +sub have_registered_component { + my ( $self, $cmp_seq_region ) = @_; + + if ( !defined($cmp_seq_region) ) { + throw('cmp_seq_region argument is required'); + } + + if ( exists( $self->{'cmp_register'}->{$cmp_seq_region} ) ) { + return 1; + } + + return 0; +} + +=head2 have_registered_assembled + + Arg [1] : string $asm_seq_region + The name of the sequence region to check for + registration. + Arg [2] : int $chunk_id + The chunk number of the provided seq_region to check + for registration. + Example : if ( $asm_mapper->have_registered_component( 'X', 9 ) ) { } + Description: Returns true if a given assembled region chunk + has been registered with this assembly mapper. + This should only be called by this class or the + AssemblyMapperAdaptor. In other words, do not use + this method unless you really know what you are + doing. + Return type: Boolean (0 or 1) + Exceptions : Throws on incorrect arguments + Caller : Internal, AssemblyMapperAdaptor + Status : Stable + +=cut + +sub have_registered_assembled { + my ( $self, $asm_seq_region, $chunk_id ) = @_; + + if ( !defined($asm_seq_region) ) { + throw('asm_seq_region argument is required'); + } + if ( !defined($chunk_id) ) { + throw('chunk_id is required'); + } + + if ( + exists( $self->{'asm_register'}->{$asm_seq_region}->{$chunk_id} ) ) + { + return 1; + } + + return 0; +} + + +=head2 register_component + + Arg [1] : integer $cmp_seq_region + The dbID of the component sequence region to + register. + Example : $asm_mapper->register_component('AL312341.1'); + Description: Flags a given component sequence region as registered + in this assembly mapper. This should only be called + by this class or the AssemblyMapperAdaptor. + Return type: None + Exceptions : Throws on incorrect arguments + Caller : Internal, AssemblyMapperAdaptor + Status : Stable + +=cut + +sub register_component { + my ( $self, $cmp_seq_region ) = @_; + + if ( !defined($cmp_seq_region) ) { + throw('cmp_seq_region argument is required'); + } + + $self->{'cmp_register'}->{$cmp_seq_region} = 1; +} + +=head2 register_assembled + + Arg [1] : integer $asm_seq_region + The dbID of the sequence region to register. + Arg [2] : int $chunk_id + The chunk number of the provided seq_region to register. + Example : $asm_mapper->register_assembled( 'X', 4 ); + Description: Flags a given assembled region as registered in this + assembly mapper. This should only be called by this + class or the AssemblyMapperAdaptor. Do not call this + method unless you really know what you are doing. + Return type: None + Exceptions : Throws on incorrect arguments + Caller : Internal, AssemblyMapperAdaptor + Status : Stable + +=cut + +sub register_assembled { + my ( $self, $asm_seq_region, $chunk_id ) = @_; + + if ( !defined($asm_seq_region) ) { + throw('asm_seq_region argument is required'); + } + if ( !defined($chunk_id) ) { + throw('chunk_id srgument is required'); + } + + $self->{'asm_register'}->{$asm_seq_region}->{$chunk_id} = 1; +} + +=head2 mapper + + Arg [1] : None + Example : $mapper = $asm_mapper->mapper(); + Description: Retrieves the internal mapper used by this Assembly + Mapper. This is unlikely to be useful unless you + _really_ know what you are doing. + Return type: Bio::EnsEMBL::Mapper + Exceptions : None + Caller : Internal, AssemblyMapperAdaptor + Status : Stable + +=cut + +sub mapper { + my ($self) = @_; + + return $self->{'mapper'}; +} + +=head2 assembled_CoordSystem + + Arg [1] : None + Example : $cs = $asm_mapper->assembled_CoordSystem(); + Description: Retrieves the assembled CoordSystem from this + assembly mapper. + Return type: Bio::EnsEMBL::CoordSystem + Exceptions : None + Caller : Internal, AssemblyMapperAdaptor + Status : Stable + +=cut + +sub assembled_CoordSystem { + my ($self) = @_; + + return $self->{'asm_cs'}; +} + +=head2 component_CoordSystem + + Arg [1] : None + Example : $cs = $asm_mapper->component_CoordSystem(); + Description: Retrieves the component CoordSystem from this + assembly mapper. + Return type: Bio::EnsEMBL::CoordSystem + Exceptions : None + Caller : Internal, AssemblyMapperAdaptor + Status : Stable + +=cut + +sub component_CoordSystem { + my ($self) = @_; + + return $self->{'cmp_cs'}; +} + +=head2 adaptor + + Arg [1] : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor $adaptor + Description: Getter/set terfor this object's database adaptor. + Returntype : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor + Exceptions : None + Caller : General + Status : Stable + +=cut + +sub adaptor { + my ( $self, $value ) = @_; + + if ( defined($value) ) { + weaken($self->{'adaptor'} = $value); + } + + return $self->{'adaptor'}; +} + +=head2 in_assembly + + Description: DEPRECATED, use map() or list_ids() instead. + +=cut + +sub in_assembly { + my ( $self, $object ) = @_; + + deprecate('Use map() or list_ids() instead.'); + + my $csa = $self->db->get_CoordSystemAdaptor(); + + my $top_level = $csa->fetch_top_level(); + + my $asma = + $self->adaptor->fetch_by_CoordSystems( $object->coord_system(), + $top_level ); + + my @list = $asma->list_ids( $object->seq_region(), + $object->start(), + $object->end(), + $object->coord_system() ); + + return ( @list > 0 ); +} + +=head2 map_coordinates_to_assembly + + Description: DEPRECATED, use map() instead. + +=cut + +sub map_coordinates_to_assembly { + my ( $self, $contig_id, $start, $end, $strand ) = @_; + + deprecate('Use map() instead.'); + + # Not sure if contig_id is seq_region_id or name... + return + $self->map( $contig_id, $start, $end, $strand, + $self->contig_CoordSystem() ); + +} + +=head2 fast_to_assembly + + Description: DEPRECATED, use map() instead. + +=cut + +sub fast_to_assembly { + my ( $self, $contig_id, $start, $end, $strand ) = @_; + + deprecate('Use map() instead.'); + + # Not sure if contig_id is seq_region_id or name... + return + $self->map( $contig_id, $start, $end, $strand, + $self->contig_CoordSystem() ); +} + +=head2 map_coordinates_to_rawcontig + + Description: DEPRECATED, use map() instead. + +=cut + +sub map_coordinates_to_rawcontig { + my ( $self, $chr_name, $start, $end, $strand ) = @_; + + deprecate('Use map() instead.'); + + return + $self->map( $chr_name, $start, $end, $strand, + $self->assembled_CoordSystem() ); +} + +=head2 list_contig_ids + + Description: DEPRECATED, use list_ids() instead. + +=cut + +sub list_contig_ids { + my ( $self, $chr_name, $start, $end ) = @_; + + deprecate('Use list_ids() instead.'); + + return + $self->list_ids( $chr_name, $start, $end, + $self->assembled_CoordSystem() ); +} + +1;