[ensembl-dev] Bug report and fix to variant_effect_predictor.pl

[Aliz Raksi]

Dear Ensembl team,

I am writing to report a bug in *variant_effect_predictor.pl* version 2.4.
If you run the script with the optional parameter *-o stdout,* then "quiet"
mode is forced too late in the program, and undesired debug statements are
written in the beginning of the output.
The API version used is 66.

PROPOSED FIX:

Move line 794 (*debug("Reading configuration from $file") unless
defined($config->{quiet});*)
to line 809, i.e. to after the *while(<CONFIG>) {...} *statement.

Move lines 394-398:
    # force quiet if outputting to STDOUT
    if(defined($config->{output_file}) && $config->{output_file} =~
/stdout/i) {
        delete $config->{verbose} if defined($config->{verbose});
        $config->{quiet} = 1;
    }
to line 807, i.e. to between the *while(<CONFIG>) {...}* statement and the
new location of the just-moved debug statement.

Therefore, the subroutine *read_config_from_file* should look like this:

# reads config from a file
sub read_config_from_file {
    my $config = shift;
    my $file = shift;

    open CONFIG, $file or die "ERROR: Could not open config file
\"$file\"\n";

    while(<CONFIG>) {
        next if /^\#/;
        my @split = split /\s+|\=/;
        my $key = shift @split;
        $key =~ s/^\-//g;

        if(defined($config->{$key}) && ref($config->{$key}) eq 'ARRAY') {
            push @{$config->{$key}}, @split;
        }
        else {
            $config->{$key} ||= $split[0];
        }
    }

    # force quiet if outputting to STDOUT
    if(defined($config->{output_file}) && $config->{output_file} =~
/stdout/i) {
        delete $config->{verbose} if defined($config->{verbose});
        $config->{quiet} = 1;
    }

    debug("Reading configuration from $file") unless
defined($config->{quiet});

    close CONFIG;
}

Finally, some debug statements don't check for whether we're in quiet mode.
Change those occurences of *debug("...");* to
*debug("...") unless defined($config->{quiet});*

This occurs at the following lines:
838    debug("Failed to compile plugin $module: $@");
850    debug("Failed to instantiate plugin $module: $@");
869    debug("Warning: plugin $plugin version ($plugin_version) does not
match the current VEP version ($VERSION)");
874    debug("Warning: plugin $plugin does not define a version number");
878    debug("You may experience unexpected behaviour with this plugin")
unless $version_ok;
884    debug("Plugin $module doesn't implement a required method
'$required', does it inherit from BaseVepPlugin?");
893    debug("Loaded plugin: $module");
898    debug("Fetching regulatory features for plugin: $module");


Sincerely,
Aliz R. Rao

UCLA Geffen School of Medicine
Department of Human Genetics, Nelson Lab
695 Charles E Young Drive S
Gonda 5554A

Los Angeles CA 90095-8348 USA

alizrrao at gmail.com

714.548.1133
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