Class FastqReader

    • Constructor Detail

      • FastqReader

        public FastqReader​(File file)
      • FastqReader

        public FastqReader​(File file,
                           boolean skipBlankLines)
        Constructor
        Parameters:
        file - of FASTQ to read read. Will be opened with htsjdk.samtools.util.IOUtil.openFileForBufferedReading
        skipBlankLines - should we skip blank lines ?
      • FastqReader

        public FastqReader​(File file,
                           BufferedReader reader,
                           boolean skipBlankLines)
        Constructor
        Parameters:
        file - Name of FASTQ being read, or null if not known.
        reader - input reader . Will be closed by the close method
        skipBlankLines - should we skip blank lines ?
    • Method Detail

      • iterator

        public Iterator<FastqRecord> iterator()
        WARNING: Despite the fact that this class implements Iterable, calling iterator() method does not start iteration from the beginning of the file. Developers should probably not call iterator() directly. It is provided so that this class can be used in Java for-each loop.
        Specified by:
        iterator in interface Iterable<FastqRecord>
      • getLineNumber

        public int getLineNumber()
      • getFile

        public File getFile()
        Returns:
        Name of FASTQ being read, or null if not known.
      • checkLine

        protected void checkLine​(String line,
                                 FastqReader.LineType kind)
        Checks that the line is neither null (representing EOF) or empty (blank line in file).
      • error

        protected String error​(String msg)
        Generates an error message with line number information.