[Bioperl-l] RepeatMasker

Robert Hubley rhubley at systemsbiology.org
Tue Jul 7 13:58:01 UTC 2009

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?



|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?
||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 

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