Reading gene sequences close to the chromosome border

[LIBRARY] Configuration
Mode: RH
PWM: No
RT MIN: 200
RT MAX: 5500

Processing Fragments ********** OK (00:03:57)
34569813 mol: in 34569746, new 67, out 34565024
avg Len 214.94418, maxLen 744
start amplification
[INFO] Loading default PCR distribution
preparing transcript sequences ******* ERROR
[ERROR] Error while preparing sequences: Problems reading sequence Chr3: pos -1, len 100,
check whether chromosomal sequence exists / has the correct size
java.lang.RuntimeException: Problems reading sequence Chr3: pos -1, len 100,
check whether chromosomal sequence exists / has the correct size
at barna.model.Graph.readSequence(Graph.java:585)
at barna.model.Graph.readSequence(Graph.java:473)
at barna.model.Transcript.getSplicedSequence(Transcript.java:459)
at barna.flux.simulator.fragmentation.Fragmenter.getMapTxSeq(Fragmenter.java:375)
at barna.flux.simulator.fragmentation.Fragmenter.process(Fragmenter.java:539)
at barna.flux.simulator.fragmentation.Fragmenter.call(Fragmenter.java:258)
at barna.flux.simulator.SimulationPipeline.call(SimulationPipeline.java:424)
at barna.flux.simulator.SimulationPipeline.call(SimulationPipeline.java:53)
at barna.commons.launcher.Flux.main(Flux.java:212)
Caused by: java.lang.NegativeArraySizeException
at barna.model.Graph.readSequence(Graph.java:507)
at barna.model.Graph.readSequence(Graph.java:473)
at barna.model.Graph.readSequence(Graph.java:529)
... 8 more
FAILED