int peptideStart = peptide.getStartIndex()
+ peptide.getGeneInfo().getStart();
if (bedWriter != null && !foundProteins.contains(proteinName)) {
foundProteins.add(proteinName);
BedLineOutputter bedLineOutputter = new BedLineOutputter(
peptide, proteinName);
bedWriter.write(bedLineOutputter.toString());
}
if (DebuggingFlag.get_use_mascot_score_flag() == 1) {
int mapq = result.getConfidenceScore()
.round(new MathContext(0)).intValue();