return yes ? "yes\n" : "no\n";
}
public String getQualimapCmdLine(boolean drawChromosomeLimits) {
CommandLineBuilder cmdBuilder = new CommandLineBuilder("qualimap " + Constants.TOOL_NAME_BAMQC);
cmdBuilder.append(Constants.BAMQC_OPTION_BAM_FILE, bamFile);
if (featureFile != null) {
cmdBuilder.append(Constants.BAMQC_OPTION_GFF_FILE, featureFile);
if (computeOutsideStats) {
cmdBuilder.append(Constants.BAMQC_OPTION_OUTSIDE_STATS);
}
}
if (drawChromosomeLimits) {
cmdBuilder.append(Constants.BAMQC_OPTION_PAINT_CHROMOSOMES);
}
cmdBuilder.append(Constants.BAMQC_OPTION_NUM_WINDOWS, numberOfWindows);
cmdBuilder.append(Constants.BAMQC_OPTION_MIN_HOMOPOLYMER_SIZE, minHomopolymerSize);
return cmdBuilder.getCmdLine();
}