<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">send it to <a href="mailto:dev@ensembl.org">dev@ensembl.org</a><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Lucida Grande'; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Lucida Grande'; font-size: 10px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><p class="MsoNormal"><font class="Apple-style-span" face="'Devanagari MT'" size="7"><span class="Apple-style-span" style="font-size: 27px; "><font class="Apple-style-span" face="'Lucida Grande'" size="3"><span class="Apple-style-span" style="font-size: 12px; "><br class="Apple-interchange-newline"></span></font><font class="Apple-style-span" size="5"><span class="Apple-style-span" style="font-size: 18px; ">ॐ</span></font></span></font></p></span><p></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 6px; margin-left: 0px; line-height: 19px; font: normal normal normal 16px/normal Helvetica; "><span class="Apple-style-span" style="font-family: 'Lucida Grande'; font-size: 10px; ">Michael Yourshaw</span></p><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">UCLA Geffen School of Medicine</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">Department of Human Genetics, Nelson Lab</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">695 Charles E Young Drive S</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">Gonda 5554</span></div><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 3px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">Los Angeles CA 90095-8348 USA</span></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 3px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; color: rgb(0, 0, 153); "><span style="text-decoration: underline; letter-spacing: 0px; "><a href="mailto:myourshaw@ucla.edu">myourshaw@ucla.edu</a></span></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 6px; margin-left: 0px; font: normal normal normal 10px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">970.691.8299</span></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 6px; margin-left: 0px; font: normal normal normal 9px/normal 'Lucida Grande'; "><span style="letter-spacing: 0px; ">This message is intended only for the use of the addressee and may contain information that is PRIVILEGED and CONFIDENTIAL, and/or may contain ATTORNEY WORK PRODUCT. If you are not the intended recipient, you are hereby notified that any dissemination of this communication is strictly prohibited. If you have received this communication in error, please erase all copies of the message and its attachments and notify us immediately. Thank you.</span></p><div><font class="Apple-style-span" size="1"><span class="Apple-style-span" style="font-size: 9px; "><br></span></font></div></span><br class="Apple-interchange-newline"><br class="Apple-interchange-newline"></span></div></span></span>
</div>
<div><br><div>Begin forwarded message:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1.0);"><b>From: </b></span><span style="font-family:'Helvetica'; font-size:medium;">Aliz Raksi <<a href="mailto:aliz0611@gmail.com">aliz0611@gmail.com</a>><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1.0);"><b>Subject: </b></span><span style="font-family:'Helvetica'; font-size:medium;"><b>Bug report and fix to vax.pl</b><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1.0);"><b>Date: </b></span><span style="font-family:'Helvetica'; font-size:medium;">April 24, 2012 12:52:11 PM PDT<br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1.0);"><b>To: </b></span><span style="font-family:'Helvetica'; font-size:medium;">"Yourshaw, Michael (BOL)" <<a href="mailto:myourshaw@ucla.edu">myourshaw@ucla.edu</a>><br></span></div><br>Hi Michael,<br>Who should I send the <a href="http://vax.pl/">vax.pl</a> bug report to? Can you give me an email address? - Aliz<br><br>------------------------------------------------------------------------<br><br><br>To whom it may concern,<br>
<br>I am writing to report a bug in <a href="http://vax.pl/">vax.pl</a>. If you run the script with the optional parameter <i>-o stdout,</i> then "quiet" mode is forced too late in the program, and undesired debug statements are written in the beginning of the output.<br>
<br>PROPOSED FIX:<br><br>Move line 794 (<i>debug("Reading configuration from $file") unless defined($config->{quiet});</i>)<br>to line 809, i.e. to after the <i>while(<CONFIG>) {...} </i>statement.<br><br>
Move lines 394-398:<br> <span style="font-family:georgia,serif"> # force quiet if outputting to STDOUT</span><br style="font-family:georgia,serif"><span style="font-family:georgia,serif"> if(defined($config->{output_file}) && $config->{output_file} =~ /stdout/i) {</span><br style="font-family:georgia,serif">
<span style="font-family:georgia,serif"> delete $config->{verbose} if defined($config->{verbose});</span><br style="font-family:georgia,serif"><span style="font-family:georgia,serif"> $config->{quiet} = 1;</span><br style="font-family:georgia,serif">
<span style="font-family:georgia,serif"> }</span><br style="font-family:georgia,serif">to line 807, i.e. to between the <i>while(<CONFIG>) {...}</i> statement and the debug statement, which was moved in the previous step.<br>
<br>Therefore, the subroutine <i>read_config_from_file</i> should look like this:<br><br><span style="font-family:georgia,serif"># reads config from a file</span><br style="font-family:georgia,serif"><span style="font-family:georgia,serif">sub read_config_from_file {</span><br style="font-family:georgia,serif">
<span style="font-family:georgia,serif"> my $config = shift;</span><br style="font-family:georgia,serif"><span style="font-family:georgia,serif"> my $file = shift;</span><br style="font-family:georgia,serif"><span style="font-family:georgia,serif"> </span><br style="font-family:georgia,serif">
<span style="font-family:georgia,serif"> open CONFIG, $file or die "ERROR: Could not open config file \"$file\"\n";</span><br style="font-family:georgia,serif"><span style="font-family:georgia,serif"> </span><br style="font-family:georgia,serif">
<span style="font-family:georgia,serif"> while(<CONFIG>) {</span><br style="font-family:georgia,serif"><span style="font-family:georgia,serif"> next if /^\#/;</span><br style="font-family:georgia,serif"><span style="font-family:georgia,serif"> my @split = split /\s+|\=/;</span><br style="font-family:georgia,serif">
<span style="font-family:georgia,serif"> my $key = shift @split; </span><br style="font-family:georgia,serif"><span style="font-family:georgia,serif"> $key =~ s/^\-//g;</span><br style="font-family:georgia,serif">
<span style="font-family:georgia,serif"> </span><br style="font-family:georgia,serif"><span style="font-family:georgia,serif"> if(defined($config->{$key}) && ref($config->{$key}) eq 'ARRAY') {</span><br style="font-family:georgia,serif">
<span style="font-family:georgia,serif"> push @{$config->{$key}}, @split;</span><br style="font-family:georgia,serif"><span style="font-family:georgia,serif"> }</span><br style="font-family:georgia,serif">
<span style="font-family:georgia,serif"> else {</span><br style="font-family:georgia,serif"><span style="font-family:georgia,serif"> $config->{$key} ||= $split[0];</span><br style="font-family:georgia,serif">
<span style="font-family:georgia,serif"> }</span><br style="font-family:georgia,serif"><span style="font-family:georgia,serif"> }</span><br style="font-family:georgia,serif"><span style="font-family:georgia,serif"> </span><br style="font-family:georgia,serif">
<span style="font-family:georgia,serif"> # force quiet if outputting to STDOUT</span><br style="font-family:georgia,serif"><span style="font-family:georgia,serif"> if(defined($config->{output_file}) && $config->{output_file} =~ /stdout/i) {</span><br style="font-family:georgia,serif">
<span style="font-family:georgia,serif"> delete $config->{verbose} if defined($config->{verbose});</span><br style="font-family:georgia,serif"><span style="font-family:georgia,serif"> $config->{quiet} = 1;</span><br style="font-family:georgia,serif">
<span style="font-family:georgia,serif"> }</span><br style="font-family:georgia,serif"><span style="font-family:georgia,serif"> </span><br style="font-family:georgia,serif"><span style="font-family:georgia,serif"> debug("Reading configuration from $file") unless defined($config->{quiet});</span><br style="font-family:georgia,serif">
<span style="font-family:georgia,serif"> </span><br style="font-family:georgia,serif"><span style="font-family:georgia,serif"> close CONFIG;</span><br style="font-family:georgia,serif"><span style="font-family:georgia,serif">}</span><br>
<br>Finally, some debug statements don't check for whether we're in quiet mode. Change those occurences of <i>debug("...");</i> to<br><i>debug("...") unless defined($config->{quiet});</i><br>
<br>This occurs at the following lines:<br><span style="font-family:georgia,serif">838 debug("Failed to compile plugin $module: $@");</span><br style="font-family:georgia,serif"><span style="font-family:georgia,serif">850 debug("Failed to instantiate plugin $module: $@");</span><br style="font-family:georgia,serif">
<span style="font-family:georgia,serif">869 debug("Warning: plugin $plugin version ($plugin_version) does not match the current VEP version ($VERSION)");</span><br style="font-family:georgia,serif"><span style="font-family:georgia,serif">874 debug("Warning: plugin $plugin does not define a version number");</span><br style="font-family:georgia,serif">
<span style="font-family:georgia,serif">878 debug("You may experience unexpected behaviour with this plugin") unless $version_ok;</span><br style="font-family:georgia,serif"><span style="font-family:georgia,serif">884 debug("Plugin $module doesn't implement a required method '$required', does it inherit from BaseVepPlugin?");</span><br style="font-family:georgia,serif">
<span style="font-family:georgia,serif">893 debug("Loaded plugin: $module");</span><br style="font-family:georgia,serif"><span style="font-family:georgia,serif">898 debug("Fetching regulatory features for plugin: $module");</span><br>
<br><br>Sincerely,<br>Aliz R. Rao<br><br><span style="font-family:Helvetica;font-size:12px"><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;font-size:12px;white-space:normal;font-family:Helvetica;word-spacing:0px"><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;font-size:12px;white-space:normal;font-family:Helvetica;word-spacing:0px"><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font:normal normal normal 10px/normal 'Lucida Grande'">
<span style="letter-spacing:0px">UCLA Geffen School of Medicine</span></div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font:normal normal normal 10px/normal 'Lucida Grande'"><span style="letter-spacing:0px">Department of Human Genetics, <span class="il">Nelson</span> Lab</span></div>
<div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font:normal normal normal 10px/normal 'Lucida Grande'"><span style="letter-spacing:0px">695 Charles E Young Drive S</span></div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font:normal normal normal 10px/normal 'Lucida Grande'">
<span style="letter-spacing:0px">Gonda 5554A</span></div><p style="margin-top:0px;margin-right:0px;margin-bottom:3px;margin-left:0px;font:normal normal normal 10px/normal 'Lucida Grande'"><span style="letter-spacing:0px">Los Angeles CA 90095-8348 USA</span></p><p style="margin-top:0px;margin-right:0px;margin-bottom:3px;margin-left:0px;font:normal normal normal 10px/normal 'Lucida Grande';color:rgb(0,0,153)"><span style="text-decoration:underline;letter-spacing:0px"><a href="mailto:alizrrao@gmail.com" target="_blank">alizrrao@gmail.com</a></span></p><p style="margin-top:0px;margin-right:0px;margin-bottom:6px;margin-left:0px;font:normal normal normal 10px/normal 'Lucida Grande'"><span style="letter-spacing:0px"><a href="tel:714.548.1133" value="+19706918299" target="_blank">714.548.1133</a></span></p>
</span></span></span><br>
</blockquote></div><br></body></html>