setFileLogger(logFileName);
}
if (DebuggingFlag.get_sbi_debug_flag() == 1) {
File translationTableFile = new File(line.getOptionValue("t"));
SamifierRunner samifier = new SamifierRunner(
searchResultsPaths, genomeFile, mapFile, chromosomeDir,
outfile, bedfilePath, confidenScore,
translationTableFile);
samifier.run();
} else {
SamifierRunner samifier = new SamifierRunner(
searchResultsPaths, genomeFile, mapFile, chromosomeDir,
outfile, bedfilePath, confidenScore);
samifier.run();
}
} catch (ParseException pe) {
System.err.println(pe);
System.err.println("Version = " + VERSION);