public SequencesWriter(SequenceDataSource source,File outputDir,long sizeLimit,Collection<String> namesToExclude,PrereadType type,boolean compressed,Integer trimQualityThreshold){
  mDataSource=source;
  mOutputDir=outputDir;
  mPrereadType=type;
  mSdfId=new SdfId();
  if (mDataSource == null) {
    throw new NullPointerException("Provided data source was null.");
  }
  FileUtils.ensureOutputDirectory(mOutputDir);
  mSizeLimit=sizeLimit;
  mNamesToExclude=namesToExclude == null ? new ArrayList<>() : namesToExclude;
  mCompressed=compressed;
  if (trimQualityThreshold != null) {
    if (System.getProperty("quality-window-size") != null) {
      final int windowSize=Integer.parseInt(System.getProperty("quality-window-size"));
      mReadTrimmer=new DefaultReadTrimmer(windowSize,trimQualityThreshold);
      Diagnostic.userLog("Performing trimming with quality threshold " + trimQualityThreshold + " window size "+ windowSize);
    }
 else {
      mReadTrimmer=new BestSumReadTrimmer(trimQualityThreshold);
      Diagnostic.userLog("Performing trimming with BestSum, threshold " + trimQualityThreshold);
    }
  }
 else {
    mReadTrimmer=new NullReadTrimmer();
  }
}

public SequencesWriter ( SequenceDataSource source , File outputDir , long sizeLimit , Collection < String > namesToExclude , PrereadType type , boolean compressed , Integer trimQualityThreshold ) { mDataSource = source ; mOutputDir = outputDir ; mPrereadType = type ; mSdfId = new SdfId ( ) ; if ( mDataSource == null ) { throw new NullPointerException ( "Provided data source was null." ) ; } FileUtils . ensureOutputDirectory ( mOutputDir ) ; mSizeLimit = sizeLimit ; mNamesToExclude = namesToExclude == null ? new ArrayList < > ( ) : namesToExclude ; mCompressed = compressed ; if ( trimQualityThreshold != null ) { if ( System . getProperty ( "quality-window-size" ) != null ) { final int windowSize = Integer . parseInt ( System . getProperty ( "quality-window-size" ) ) ; mReadTrimmer = new DefaultReadTrimmer ( windowSize , trimQualityThreshold ) ; Diagnostic . userLog ( "Performing trimming with quality threshold " + trimQualityThreshold + " window size " + windowSize ) ; } else { mReadTrimmer = new BestSumReadTrimmer ( trimQualityThreshold ) ; Diagnostic . userLog ( "Performing trimming with BestSum, threshold " + trimQualityThreshold ) ; } } else { mReadTrimmer = new NullReadTrimmer ( ) ; } }
creates a writer for processing sequences from provided data source .
