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Commit 6d00c980 authored by Ian Longden's avatar Ian Longden
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more fixes plus lots of print STDERR which will be removed when happy

parent 445acd25
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Showing with 40 additions and 27 deletions
modules/Bio/EnsEMBL/AssemblyMapper.pm
View file @ 6d00c980
......@@ -213,6 +213,8 @@ sub map {
push @tmp, $frm_seq_region_name;
my $seq_region_id = @{$self->adaptor()->seq_regions_to_ids($frm_cs, \@tmp)}[0];
print STDERR "name = $frm_seq_region_name, id = $seq_region_id \n";
#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
......@@ -239,6 +241,8 @@ sub map {
" of this AssemblyMapper");
}
print STDERR "seq region id is $seq_region_id\n";
print STDERR "mapper is of type ".ref($mapper)."\n";
return $mapper->map_coordinates($seq_region_id, $frm_start, $frm_end,
$frm_strand, $frm);
}
......
modules/Bio/EnsEMBL/ChainedAssemblyMapper.pm
View file @ 6d00c980
......@@ -332,10 +332,13 @@ sub map {
}
if($fastmap) {
print STDERR "FAST seq region id is $seq_region_id\n";
return $mapper->fastmap($seq_region_id, $frm_start, $frm_end,
$frm_strand, $frm);
}
print STDERR "mapper is of type ".ref($mapper)."\n";
print STDERR "SLOW seq region id is $seq_region_id\n";
return $mapper->map_coordinates($seq_region_id, $frm_start, $frm_end,
$frm_strand, $frm);
}
......
modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm
View file @ 6d00c980
......@@ -250,6 +250,12 @@ sub register_assembled {
my $asm_start = shift;
my $asm_end = shift;
my $test = $asm_seq_region;
$test =~ s/\d+//g;
if(length($test) > 0 or $asm_seq_region < 1000){
print STDERR "$asm_seq_region NOT INTEGER\n";
print STDERR stack_trace_dump();
}
if(!ref($asm_mapper) || !$asm_mapper->isa('Bio::EnsEMBL::AssemblyMapper')) {
throw("Bio::EnsEMBL::AssemblyMapper argument expected");
}
......@@ -373,12 +379,12 @@ sub register_assembled {
# Load the unregistered regions of the mapper
#
while($sth->fetch()) {
next if($asm_mapper->have_registered_component($cmp_seq_region));
$asm_mapper->register_component($cmp_seq_region);
next if($asm_mapper->have_registered_component($cmp_seq_region_id));
$asm_mapper->register_component($cmp_seq_region_id);
$asm_mapper->mapper->add_map_coordinates(
$asm_seq_region, $asm_start, $asm_end,
$ori,
$cmp_seq_region, $cmp_start, $cmp_end);
$cmp_seq_region_id, $cmp_start, $cmp_end);
my $arr = [ $cmp_seq_region_id, $cmp_seq_region,
$cmp_cs_id, $cmp_seq_region_length ];
......@@ -766,14 +772,14 @@ sub register_chained {
$start_mid_mapper->add_map_coordinates
(
$seq_region_id,$start_start, $start_end, $ori,
$mid_seq_region, $mid_start, $mid_end
$mid_seq_region_id, $mid_start, $mid_end
);
} else {
if( $from eq "first" ) {
$combined_mapper->add_map_coordinates
(
$seq_region_id,$start_start, $start_end, $ori,
$mid_seq_region, $mid_start, $mid_end
$mid_seq_region_id, $mid_start, $mid_end
);
} else {
$combined_mapper->add_map_coordinates
......@@ -811,7 +817,7 @@ sub register_chained {
# last_registry and we are done
if( ! defined $mid_cs ) {
for my $range ( @mid_ranges ) {
$end_registry->check_and_register( $range->[1], $range->[2],
$end_registry->check_and_register( $range->[0], $range->[2],
$range->[3] );
}
......@@ -870,8 +876,8 @@ sub register_chained {
# "$mid_start-$mid_end($ori)\n";
$end_mid_mapper->add_map_coordinates
(
$end_seq_region, $end_start, $end_end, $ori,
$mid_seq_region, $mid_start, $mid_end
$end_seq_region_id, $end_start, $end_end, $ori,
$mid_seq_region_id, $mid_start, $mid_end
);
#update sr_name cache
......@@ -881,7 +887,7 @@ sub register_chained {
$self->{'sr_id_cache'}->{"$end_seq_region_id"} = $arr;
#register this region on the end coord system
$end_registry->check_and_register($end_seq_region, $end_start, $end_end);
$end_registry->check_and_register($end_seq_region_id, $end_start, $end_end);
}
}
......@@ -975,11 +981,11 @@ sub register_all {
my %asm_registered;
while($sth->fetch()) {
$mapper->register_component($cmp_seq_region);
$mapper->register_component($cmp_seq_region_id);
$mapper->mapper->add_map_coordinates(
$asm_seq_region, $asm_start, $asm_end,
$asm_seq_region_id, $asm_start, $asm_end,
$ori,
$cmp_seq_region, $cmp_start, $cmp_end);
$cmp_seq_region_id, $cmp_start, $cmp_end);
my $arr = [$cmp_seq_region_id, $cmp_seq_region, $cmp_cs_id, $cmp_length];
......@@ -987,13 +993,13 @@ sub register_all {
$self->{'sr_id_cache'}->{"$cmp_seq_region_id"} = $arr;
# only register each asm seq_region once since it requires some work
if(!$asm_registered{$asm_seq_region}) {
$asm_registered{$asm_seq_region} = 1;
if(!$asm_registered{$asm_seq_region_id}) {
$asm_registered{$asm_seq_region_id} = 1;
# register all chunks from start of seq region to end
my $end_chunk = $asm_length >> $CHUNKFACTOR;
for(my $i = 0; $i <= $end_chunk; $i++) {
$mapper->register_assembled($asm_seq_region, $i);
$mapper->register_assembled($asm_seq_region_id, $i);
}
$arr = [$asm_seq_region_id, $asm_seq_region, $asm_cs_id, $asm_length];
......@@ -1137,15 +1143,15 @@ sub register_all_chained {
while($sth->fetch()) {
$mapper->add_map_coordinates
(
$start_seq_region, $start_start, $start_end, $ori,
$mid_seq_region, $mid_start, $mid_end
$start_seq_region_id, $start_start, $start_end, $ori,
$mid_seq_region_id, $mid_start, $mid_end
);
push( @ranges, [$start_seq_region, $start_start, $start_end ] );
push( @ranges, [$start_seq_region_id, $start_start, $start_end ] );
$reg->check_and_register( $start_seq_region, 1, $start_length );
$reg->check_and_register( $start_seq_region_id, 1, $start_length );
if( ! defined $mid_cs ) {
$casm_mapper->last_registry()->check_and_register
( $mid_seq_region, $mid_start, $mid_end );
( $mid_seq_region_id, $mid_start, $mid_end );
}
my $arr = [ $mid_seq_region_id, $mid_seq_region,
......@@ -1208,11 +1214,11 @@ sub register_all_chained {
while($sth->fetch()) {
$end_mid_mapper->add_map_coordinates
(
$end_seq_region, $end_start, $end_end, $ori,
$mid_seq_region, $mid_start, $mid_end
$end_seq_region_id, $end_start, $end_end, $ori,
$mid_seq_region_id, $mid_start, $mid_end
);
$reg->check_and_register( $end_seq_region, 1, $end_length );
$reg->check_and_register( $end_seq_region_id, 1, $end_length );
my $arr = [ $end_seq_region_id, $end_seq_region,
$end_cs_id, $end_length ];
......@@ -1242,11 +1248,11 @@ sub _build_combined_mapper {
foreach my $range (@$ranges) {
my ( $seq_region_name, $start, $end) = @$range;
my ( $seq_region_id, $start, $end) = @$range;
my $sum = 0;
my @initial_coords = $start_mid_mapper->map_coordinates($seq_region_name,
my @initial_coords = $start_mid_mapper->map_coordinates($seq_region_id,
$start,$end,1,
$start_name);
......@@ -1276,12 +1282,12 @@ sub _build_combined_mapper {
if($start_name eq 'first') { # add coords in consistant order
$combined_mapper->add_map_coordinates(
$seq_region_name, $total_start, $total_end, $ori,
$seq_region_id, $total_start, $total_end, $ori,
$fcoord->id(), $fcoord->start(), $fcoord->end());
} else {
$combined_mapper->add_map_coordinates(
$fcoord->id(), $fcoord->start(), $fcoord->end(),$ori,
$seq_region_name, $total_start, $total_end);
$seq_region_id, $total_start, $total_end);
}
#print STDERR " fcoord: id=".$fcoord->id." start=".
......
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