String bamPath = settingsDlg.getBamFilePath();
String gffPath = settingsDlg.getGtfFilePath();
ComputeCountsTask computeCountsTask = new ComputeCountsTask(bamPath, gffPath);
LibraryProtocol p = LibraryProtocol.getProtocolByName(settingsDlg.getProtocol());
computeCountsTask.setProtocol(p);
computeCountsTask.setCountingAlgorithm(settingsDlg.getCountingAlgorithm());
computeCountsTask.addSupportedFeatureType(ComputeCountsTask.EXON_TYPE_ATTR);
computeCountsTask.setAttrName(ComputeCountsTask.GENE_ID_ATTR);