Region support: reporting bug

What steps will reproduce the problem?
1. bpipe run region.groovy test.txt
2. region.groovy is the pipe in attachment
3. test.txt is an empty file

What is the expected output? What do you see instead?

I am testing region feature: I want to pass a series of intervals on the human 
genome. There is no documentation on this part so I am try to guess ....

I got:

================================================================================
====================
|                              Starting Pipeline at 2013-10-22 15:04            
                   |
================================================================================
====================
Sequences ordered by size are [chr1[0-249231242]]
Sequences ordered by size are [chr2[0-243160825]]
java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at org.codehaus.groovy.tools.GroovyStarter.rootLoader(GroovyStarter.java:106)
    at org.codehaus.groovy.tools.GroovyStarter.main(GroovyStarter.java:128)
Caused by: java.lang.IllegalStateException: Bisecting distance between genes 
produced a location inside the lower gene. Please report this as a bug.
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
    at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:77)
    at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrapNoCoerce.callConstructor(ConstructorSite.java:102)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:57)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:182)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:190)
    at bpipe.Sequence.split(Sequence.groovy:132)

[CUTTED AT THE FIRST BPIPE ERROR]

In attachment the whole error (log.log)

What version of the product are you using? On what operating system?

Version 0.9.8.4

Regards
Original issue reported on code.google.com by davide.r...@gmail.com on 22 Oct 2013 at 1:09
Attachments:
pallassgj / bpipe

Region support: reporting bug #83
