private void loadAnnotations(String annotationFilename) { try { LineIterator lines = new LineIterator(new FastBufferedReader(new FileReader(annotationFilename))); for (MutableString line : lines.allLines()) { if (line.startsWith("#")) continue; String tokens[] = line.toString().split("\t"); final String chromosome = tokens[0]; int position = Integer.parseInt(tokens[1]); // convert to zero-based position used by goby/variationanalysis: position -= 1; Int2ObjectAVLTreeMap<Annotation> perPositionMap = annotations.getOrDefault(chromosome, new Int2ObjectAVLTreeMap<>()); Annotation a = new Annotation(); a.position = position; a.toBase = tokens.length >= 3 ? tokens[2] : null; a.frequency = tokens.length >= 4 ? Float.parseFloat(tokens[3]) : null; perPositionMap.put(position, a); annotations.put(chromosome, perPositionMap); } } catch (FileNotFoundException e) { throw new RuntimeException("Unable to find annotation filename:" + annotationFilename, e); } }
System.exit(1); predictionLine = new LineIterator(new FastBufferedReader(predReader));
pl.itemsName = "words"; pl.start( "Reading words..." ); final FrontCodedStringList frontCodedStringList = new FrontCodedStringList( new LineIterator( new FastBufferedReader( new InputStreamReader( zipped ? new GZIPInputStream( System.in ) : System.in, encoding ), bufferSize ), pl ), ratio, utf8 ); pl.done();
pl.itemsName = "strings"; pl.start("Reading strings..."); final FrontCodedStringList frontCodedStringList = new FrontCodedStringList(new LineIterator(new FastBufferedReader( new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding), bufferSize), pl), ratio, utf8); pl.done();
final Iterator<MutableString> iterator = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(inputStream) : inputStream, encoding), bufferSize)); final Object2LongFunction<CharSequence> function = (Object2LongFunction<CharSequence>)BinIO.loadObject(functionName); final Logger logger = LoggerFactory.getLogger(ShiftAddXorSignedStringMap.class);
final Iterator<MutableString> iterator = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(inputStream) : inputStream, encoding), bufferSize)); final Object2LongFunction<CharSequence> function = (Object2LongFunction<CharSequence>)BinIO.loadObject(functionName); final Logger logger = LoggerFactory.getLogger(ShiftAddXorSignedStringMap.class);
pl.itemsName = "words"; pl.start( "Reading words..." ); final FrontCodedStringList frontCodedStringList = new FrontCodedStringList( new LineIterator( new FastBufferedReader( new InputStreamReader( zipped ? new GZIPInputStream( System.in ) : System.in, encoding ), bufferSize ), pl ), ratio, utf8 ); pl.done();
final Iterator<MutableString> iterator = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(inputStream) : inputStream, encoding), bufferSize)); final Object2LongFunction<CharSequence> function = "-".equals(functionName) ? null : (Object2LongFunction<CharSequence>)BinIO.loadObject(functionName); final Logger logger = LoggerFactory.getLogger(LongBigListSignedStringMap.class);
final Iterator<MutableString> iterator = new LineIterator( new FastBufferedReader( new InputStreamReader( zipped ? new GZIPInputStream( inputStream ) : inputStream, encoding ), bufferSize ) ); final Object2LongFunction<CharSequence> function = (Object2LongFunction<CharSequence>)BinIO.loadObject( functionName ); LOGGER.info( "Signing..." );
final Iterator<MutableString> iterator = new LineIterator( new FastBufferedReader( new InputStreamReader( zipped ? new GZIPInputStream( inputStream ) : inputStream, encoding ), bufferSize ) ); final Object2LongFunction<CharSequence> function = (Object2LongFunction<CharSequence>)BinIO.loadObject( functionName ); LOGGER.info( "Signing..." );
pl.displayFreeMemory = true; pl.start("Loading strings..."); collection = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding)), pl).allLines(); pl.done();
pl.displayFreeMemory = true; pl.start("Loading strings..."); collection = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding)), pl).allLines(); pl.done();
pl.displayFreeMemory = true; pl.start("Loading strings..."); collection = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding)), pl).allLines(); pl.done();
pl.displayFreeMemory = true; pl.start("Loading strings..."); collection = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding)), pl).allLines(); pl.done();
pl.displayFreeMemory = true; pl.start("Loading strings..."); collection = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding)), pl).allLines(); pl.done();
pl.displayFreeMemory = true; pl.start("Loading strings..."); collection = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding)), pl).allLines(); pl.done();
pl.displayFreeMemory = true; pl.start("Loading strings..."); collection = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding)), pl).allLines(); pl.done();
pl.displayFreeMemory = true; pl.start("Loading strings..."); collection = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding)), pl).allLines(); pl.done();
pl.displayFreeMemory = true; pl.start("Loading strings..."); collection = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding)), pl).allLines(); pl.done();
pl.displayFreeMemory = true; pl.start("Loading strings..."); collection = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding)), pl).allLines(); pl.done();