Fragmenatation crashes with short transcripts (<4nt)

Issue copied from wiki post

http://sammeth.net/confluence/display/SIM/New+error+at+library+preparation+step?&#comments

The program crashes with the error for one of the four replicates (generated pro files).

[ERROR] Error while creating initial fragmentation: 0 is smaller than, or equal to, the minimum (0): m
org.apache.commons.math.exception.NotStrictlyPositiveException: 0 is smaller than, or equal to, the mi
at org.apache.commons.math.random.RandomDataImpl.nextExponential(RandomDataImpl.java:484)
at barna.flux.simulator.fragmentation.Fragmenter.processInitial(Fragmenter.java:847)
at barna.flux.simulator.fragmentation.Fragmenter.writeInitialFile(Fragmenter.java:714)
at barna.flux.simulator.fragmentation.Fragmenter.call(Fragmenter.java:180)
at barna.flux.simulator.SimulationPipeline.call(SimulationPipeline.java:440)
at barna.flux.simulator.SimulationPipeline.call(SimulationPipeline.java:54)
at barna.commons.launcher.Flux.main(Flux.java:198)

[ERROR] null
java.lang.NullPointerException
at barna.flux.simulator.fragmentation.Fragmenter.call(Fragmenter.java:181)
at barna.flux.simulator.SimulationPipeline.call(SimulationPipeline.java:440)
at barna.flux.simulator.SimulationPipeline.call(SimulationPipeline.java:54)
at barna.commons.launcher.Flux.main(Flux.java:198)