public AbstractSdfWriter(final PrereadType prereadType,final boolean hasQuality,boolean hasNames,boolean compressed,final SequenceType type){
  mPrereadType=prereadType;
  mPrereadArm=PrereadArm.UNKNOWN;
  mSdfId=new SdfId();
  mNameHandler=new SequenceNameHandler();
  mSequenceType=type;
  mFirstValid=mSequenceType.firstValid();
  mResidueCounts=new long[mSequenceType.numberKnownCodes() + mSequenceType.firstValid()];
  mNHistogram=new long[MAX_HISTOGRAM];
  mPosHistogram=new long[MAX_HISTOGRAM];
  mQSAveragePerPos=new double[MAX_HISTOGRAM];
  mPositionCounts=new long[MAX_HISTOGRAM];
  mGlobalQSAverage=0.0;
  mDataHashFunction=new PrereadHashFunction();
  mQualityHashFunction=new PrereadHashFunction();
  mNameHashFunction=new PrereadHashFunction();
  mNameSuffixHashFunction=new PrereadHashFunction();
  mHasQuality=hasQuality;
  mHasNames=hasNames;
  mCompressed=compressed;
  mSeqDataChecksum=new CRC32();
  mQualDataChecksum=new CRC32();
}

public AbstractSdfWriter ( final PrereadType prereadType , final boolean hasQuality , boolean hasNames , boolean compressed , final SequenceType type ) { mPrereadType = prereadType ; mPrereadArm = PrereadArm . UNKNOWN ; mSdfId = new SdfId ( ) ; mNameHandler = new SequenceNameHandler ( ) ; mSequenceType = type ; mFirstValid = mSequenceType . firstValid ( ) ; mResidueCounts = new long [ mSequenceType . numberKnownCodes ( ) + mSequenceType . firstValid ( ) ] ; mNHistogram = new long [ MAX_HISTOGRAM ] ; mPosHistogram = new long [ MAX_HISTOGRAM ] ; mQSAveragePerPos = new double [ MAX_HISTOGRAM ] ; mPositionCounts = new long [ MAX_HISTOGRAM ] ; mGlobalQSAverage = 0.0 ; mDataHashFunction = new PrereadHashFunction ( ) ; mQualityHashFunction = new PrereadHashFunction ( ) ; mNameHashFunction = new PrereadHashFunction ( ) ; mNameSuffixHashFunction = new PrereadHashFunction ( ) ; mHasQuality = hasQuality ; mHasNames = hasNames ; mCompressed = compressed ; mSeqDataChecksum = new CRC32 ( ) ; mQualDataChecksum = new CRC32 ( ) ; }
creates a writer for processing sequences from provided data source .
