Possible bug in barna.io.gtf.GTFwrapper.skipToNextChromosome() ?

I was running Flux Simulator 1.2.1 with the .par file parameter REF_FILE_NAME set to a GTF file containing transcripts from the mouse genome, and was seeing this message in the output:

**********[SOS] transcript ENSMUST00000082392 has no exons!

A little investigation of the Flux Simulator source code led to the method skipToNextChromosome() in the class barna.io.gtf.GTFwrapper. ENSMUST00000082392 is the first transcript in my GTF file for the chromosome "MT", and since this sequence ID matches one of the chromosome filters in the GTFwrapper.java member variable "noIDs", the code is trying to skip this chromosome.

However, when trying to fast-forward through the GTF file to the next chromosome, skipToNextChromosome() appears to add "chr" to the start of the chromosome ID for each of the lines that are being examined. Since, in my case, the method parameter "lastChrID" is set to "MT", the very next line in the GTF file is interpreted as being the start of a new chromosome (because "MT" != "chrMT").

Thus the lines in the GTF file corresponding to the mitochondrial chromosome are not in fact skipped - except for the very first line, which happens to be the first (and only) exon of ENSMUST00000082392. This behaviour subsequently leads to the SOS message I was seeing.

Note that I can work around this issue by simply renaming the chromosome "MT" to "chrMT" in my GTF file.