astalavista scorer requires chromosome names to start with "chr"

AStalavista Scorer assumes chromosome names always start with "chr". This is a problem when using reference genomes that use only the chromosome number, like the 1000 genomes project does.

When using GTF, VCF & reference sequence FASTA files that use chromosome numbers without the "chr" prefix, this Java exception occurs:

[ERROR] String index out of range: -2
java.lang.StringIndexOutOfBoundsException: String index out of range: -2
at java.lang.String.substring(String.java:1931)
at barna.astalavista.Scorer.getVariants(Scorer.java:435)
at barna.astalavista.Scorer.scoreSites(Scorer.java:1012)
at barna.astalavista.Scorer.callLoop(Scorer.java:145)
at barna.astalavista.AStalavista.call(AStalavista.java:131)
at barna.astalavista.Scorer.call(Scorer.java:134)
at barna.astalavista.Scorer.call(Scorer.java:31)
at barna.commons.launcher.Flux.main(Flux.java:198)

Note: This "chr" prefix requirement is documented on the scorer confluence wiki:
http://sammeth.net/confluence/pages/viewpage.action?pageId=5177671
but can still be considered a bug due to the prevalence of VCF files that do not use this prefix.