[Bioperl-l] RepeatMasker

Chris Fields cjfields at illinois.edu
Tue Jul 7 17:23:56 UTC 2009

Robert, the best way to handle this is to file a bug report indicating  
all the specifics as well as some example code demonstrating the  



On Jul 7, 2009, at 8:58 AM, Robert Hubley wrote:

> This list email as forwarded to us by a colleague.  I fixed this bug  
> awhile back and I just double checked 3.2.8 and don't see any  
> problems with the options -noint or -lcambig.  Could someone help us  
> determine how this is breaking bio-perl?
> Thanks,
> -Robert
> |We have told the guys at RepeatMasker that RM-3.1.6 have a problem
> |causing Bio::Tools::RepeatMasker to crash in November 2006 (Bug  
> 2138).
> |And as of today, they are now at 3.2.8, and the problem is not fixed.
> |And I don't want my project to be stalled-- any tips for a  
> workaround?
> ||
> ||Hi,
> ||
> ||Perhaps you already know about this, but in RepeatMasker 3.1.6 - 
> noint ||cannot be used because of error 'Unknown option: noint- 
> species'.
> ||This is caused by line 1131 having no space after the "-noint". || 
> Likewise, -lcambig on 1128 would probably suffer a similar problem.
> ||
> ||Will this be fixed in the next version, and how often do you  
> release new ||versions?
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