RUM aligner - perl precedence error

Question

[bioinfo89]

Hi,

I am using RUM aligner for mapping RNA-Seq data. I have used it previously also and the mapping was fine. However, currently when I use rum_runner I get the following error:

Possible precedence issue with control flow operator at /.perlbrew/libs/perl-5.26.0@lib001/bin/../lib/perl5/RUM/Common.pm line 104.

The error is related to perl but I am not sure what exactly I have to change in the Common.pm file to rectify the error.

Any help for the same would be appreciated.

Thanks!

[Titus]

you should give your command line you used. Plus this kind of error is because your files are certainly not at the good format (if you change the module you will have to change all the script part which is concerned too).

Best

[Michael]

This is a warning and can most likely be ignored. You have likely upgraded your perlbrew perl version, that is why you are seeing this warning for the first time. Obviously, if something should be changed, then it is ...at /.perlbrew/libs/perl-5.26.0@lib001/bin/../lib/perl5/RUM/Common.pm line 104. which again likely contains some code like:

return $FOO or die 'argh';

Please post this line of code if you care about removing the warning

[Jeremy Leipzig]

i don't think even the RUM people use RUM anymore

[bioinfo89]

@Michael Dondrup

The line of code in the common.pm is as under:

 98 sub isroman($) {
 99     my $arg = shift;
100     return $arg ne '' and
101         $arg =~ /^(?: M{0,3})
102                  (?: D?C{0,3} | C[DM])
103                  (?: L?X{0,3} | X[LC])
104                  (?: V?I{0,3} | I[VX])$/ix;
105 }

I could ignore the warning but the script stops showing this error.

Answer 1

[Michael]

This sub supposedly checks for presence of roman numbers, no idea why this is important for an aligner. You can simply put parentheses around the return argument and the warning should go away.

 return ($arg ne '' and $arg =~...

  /ix);

[bioinfo89]

Yes it did work!! Many Thanks!!