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Has something changed with the VEP options for —sift and —polyp hen when run offline?
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<div>I’m getting "INFO: --sift is not available for this species” message (same for polyphen) when I use it. </div>
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<div>Culpable lines appear to be (from #1833):</div>
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<div style="margin: 0px; font-family: Menlo;"> my $string = 'config_'.$tool.'_version';</div>
<div style="margin: 0px; font-family: Menlo; min-height: 14px;"> if(!defined($config->{$string}) && !defined($config->{offline})) {</div>
<div style="margin: 0px; font-family: Menlo;"> my $var_mca = $config->{reg}->get_adaptor($config->{species}, 'variation', 'metacontainer');</div>
<div style="margin: 0px; font-family: Menlo;"> my $values = $var_mca->list_value_by_key($tool.'_version') if defined($var_mca);</div>
<div style="margin: 0px; font-family: Menlo;"> $config->{$string} = $values->[0] if $values && scalar @$values;</div>
<div style="margin: 0px; font-family: Menlo;"> }</div>
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<div style="margin: 0px; font-family: Menlo;"> if(!defined($config->{$string})) {</div>
<div style="margin: 0px; font-family: Menlo;"> debug("INFO: --$tool is not available for this species") unless defined($config->{quiet});</div>
<div style="margin: 0px; font-family: Menlo;"> delete $config->{$tool};</div>
<div style="margin: 0px; font-family: Menlo;"> }</div>
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<div>Because <span style="font-family: Menlo;">$config->{config_sift_version} </span>is never set anywhere, this simply falls through the first condition into the second, removing the setting.</div>
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<div>When ran this in the debugger and manually set <span style="font-family: Menlo;">$config->{config_sift_version}</span> and <span style="font-family: Menlo;">$config->{config_polyphen_version}</span> , all seemed to work fine. It seems they should either
be set somehow, or be not required. Or maybe the first condition is supposed to test for <span style="font-family: Menlo;">defined($config->{$tool})</span> instead. </div>
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<div>I don’t know the innards of the config setup here, but any advice would be welcome. </div>
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<div>All the best</div>
<div>Stuart</div>
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<b>Stuart Watt, PhD</b></div>
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Scientific Associate</p>
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<b>Ontario Institute for Cancer Research</b></p>
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