[Bioperl-l] RepeatMasker still did not act upon Bug 2138: Any workarounds?

Sendu Bala bix at sendu.me.uk
Mon Jul 6 23:43:23 UTC 2009

John M.C. Ma wrote:
> 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?

Here's my mail to some RepeatMasker devs that they never replied to:


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 

If it really is the same bug, it should be easy to fix the latest 
version in the same way yourself.

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