Disabled automatic peak picking
@@ -84,7 +84,11 @@ public class ThermoRawImportTask extends AbstractTask {
*/
@Override
public double getFinishedPercentage() {
- return totalScans == 0 ? 0 : (double) parsedScans / totalScans;
+ if (msdkTask == null || msdkTask.getFinishedPercentage() == null) {
+ return 0.0;
+ } else {
+ return msdkTask.getFinishedPercentage().doubleValue();
+ }
}
/**
@@ -122,6 +126,8 @@ public class ThermoRawImportTask extends AbstractTask {
final String cmdLine[] = new String[]{ //
thermoRawFileParserCommand, // program to run
"-s", // output mzML to stdout
+ "-p", // no peak picking
+ "-f=1", // no index, https://github.com/compomics/ThermoRawFileParser/issues/118
"-i", // input RAW file name coming next
fileToOpen.getPath() // input RAW file name
};
