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Allow generate-names.pl to index utf8 trackLabels #1477

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Allow generate-names.pl to index utf8 trackLabels #1477

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b38dd21
Allow utf8 filenames
cmdcolin Mar 4, 2020
7778cca
Remove some print commands
cmdcolin Mar 4, 2020
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13 changes: 7 additions & 6 deletions src/perl5/Bio/JBrowse/Cmd/IndexNames.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@ use Storable ();
use File::Path ();
use File::Temp ();
use List::Util ();
use Encode qw(decode encode);

use GenomeDB ();
use Bio::GFF3::LowLevel qw/gff3_parse_feature/;
Expand Down Expand Up @@ -195,8 +196,8 @@ sub _mergeIndexEntries {

sub make_file_record {
my ( $self, $track, $file ) = @_;
-f $file or die "$file not found\n";
-r $file or die "$file not readable\n";
-f decode('UTF-8',$file) or die "$file not found\n";
-r decode('UTF-8',$file) or die "$file not readable\n";
my $gzipped = $file =~ /\.(txt|json|g)z(\.\d+)?$/;
my $type = $file =~ /\.txtz?$/ ? 'txt' :
$file =~ /\.jsonz?$/ ? 'json' :
Expand Down Expand Up @@ -364,7 +365,7 @@ sub find_names_files {
# read either names.txt or names.json files
my $name_records_iterator;
my $names_txt = File::Spec->catfile( $dir, 'names.txt' );
if( -f $names_txt ) {
if( -e decode('UTF-8',$names_txt) ) {
push @files, $self->make_file_record( $track, $names_txt );
}
else {
Expand Down Expand Up @@ -436,8 +437,8 @@ sub make_operation_stream {
#print "sizes: $self->{stats}{total_namerec_bytes}, buffered: $namerecs_buffered, b/rec: ".$total_namerec_sizes/$namerecs_buffered."\n";
$self->{stats}{avg_record_text_bytes} = $self->{stats}{total_namerec_bytes}/($self->{stats}{namerecs_buffered}||1);
$self->{stats}{total_input_bytes} = List::Util::sum(
map { my $s = -s $_->{fullpath};
$s *= 8 if $_->{fullpath} =~ /\.(g|txt|json)z$/;
map { my $s = -s decode('UTF-8',$_->{fullpath});
$s *= 8 if decode('UTF-8',$_->{fullpath}) =~ /\.(g|txt|json)z$/;
$s;
} @$names_files ) || 0;
$self->{stats}{record_stream_estimated_count} = int( $self->{stats}{total_input_bytes} / ($self->{stats}{avg_record_text_bytes}||1));;
Expand Down Expand Up @@ -710,7 +711,7 @@ sub open_names_file {
}
}
else {
open my $fh, '<', $infile or die "$! reading $infile";
open my $fh, '<', decode('UTF-8',$infile) or die "$! reading $infile";
return $fh;
}
}
Expand Down