SAMcompare errors reading in bam files

[astewart-twist]

I'm having trouble reading any kind of bam file into SAMcompare.

This is from a bam file generated by ART.

VarSim 0.5.3
21 Apr 2016 00:28:03,394  INFO [main] (SAMcompare.java:175): Reading file: art1.bam
Ignoring SAM validation error: ERROR: Record 1, Read name cl3963.ol110-20, Mapped read should have valid reference name
Ignoring SAM validation error: ERROR: Record 1, Read name cl3963.ol110-20, Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR: Record 2, Read name cl3963.ol110-19, Mapped read should have valid reference name
Ignoring SAM validation error: ERROR: Record 2, Read name cl3963.ol110-19, Alignment start should be 0 because reference name = *.
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 4
    at com.bina.varsim.fastqLiftover.types.SimulatedRead.<init>(SimulatedRead.java:43)
    at com.bina.varsim.tools.evaluation.SAMcompare.run(SAMcompare.java:195)
    at com.bina.varsim.VarSim.run(VarSim.java:74)
    at com.bina.varsim.VarSim.main(VarSim.java:33)

And this is a bam file from aligning the ART generated reads with bwa

VarSim 0.5.3
20 Apr 2016 23:46:16,293  INFO [main] (SAMcompare.java:175): Reading file: bwa1.bam
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 4
    at com.bina.varsim.fastqLiftover.types.SimulatedRead.<init>(SimulatedRead.java:43)
    at com.bina.varsim.tools.evaluation.SAMcompare.run(SAMcompare.java:195)
    at com.bina.varsim.VarSim.run(VarSim.java:74)
    at com.bina.varsim.VarSim.main(VarSim.java:33)

Any ideas?