Error with very short contig

[bartns]

Hello!

Got this error and found the cause to be a very short contig of 18bp that probably doesn't have any reads mapped. (at least after removing the contig Pilon succeeded.

Exception in thread "main" java.lang.IllegalArgumentException: Invalid reference index -1 at htsjdk.samtools.QueryInterval.<init>(QueryInterval.java:24) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:538) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.queryOverlapping(SamReader.java:400) at org.broadinstitute.pilon.BamFile.process(BamFile.scala:119) at org.broadinstitute.pilon.GenomeRegion.processBam(GenomeRegion.scala:294) at org.broadinstitute.pilon.GenomeFile.$anonfun$processRegions$5(GenomeFile.scala:105) at org.broadinstitute.pilon.GenomeFile.$anonfun$processRegions$5$adapted(GenomeFile.scala:105) at scala.collection.immutable.List.foreach(List.scala:333) at org.broadinstitute.pilon.GenomeFile.$anonfun$processRegions$4(GenomeFile.scala:105) at org.broadinstitute.pilon.GenomeFile.$anonfun$processRegions$4$adapted(GenomeFile.scala:102) at scala.collection.immutable.List.foreach(List.scala:333) at org.broadinstitute.pilon.GenomeFile.processRegions(GenomeFile.scala:102) at org.broadinstitute.pilon.Pilon$.main(Pilon.scala:111) at org.broadinstitute.pilon.Pilon.main(Pilon.scala)
Maybe similar to #65