PairedTemplateAssembler a = new PairedTemplateAssembler();
int counter = 0;
int bases = 0;
long size = 0;
Definition definition = new Definition();
definition.contentId = "input.bam".getBytes();
definition.formatMajor = 1;
definition.formatMinor = 0;
definition.magick = "CRAM".getBytes();
Format format = new FormatFactory().createFormat(definition);