Package htsjdk.samtools.fastq

Class FastqReader

java.lang.Object
htsjdk.samtools.fastq.FastqReader
All Implemented Interfaces:
Closeable, AutoCloseable, Iterable<FastqRecord>, Iterator<FastqRecord>
public class FastqReader extends Object implements Iterator<FastqRecord>, Iterable<FastqRecord>, Closeable
Reads a FASTQ file with four lines per record. 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.

  • Constructor Details

    • 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(BufferedReader reader)

    • 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 ?

    • FastqReader

      public FastqReader(File file, BufferedReader reader)

  • Method Details

    • hasNext

      public boolean hasNext()
      Specified by:
      hasNext in interface Iterator<FastqRecord>

    • next

      public FastqRecord next()
      Specified by:
      next in interface Iterator<FastqRecord>

    • remove

      public void remove()
      Specified by:
      remove in interface Iterator<FastqRecord>

    • 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.

    • close

      public void close()
      Specified by:
      close in interface AutoCloseable
      Specified by:
      close in interface Closeable

    • 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.

    • toString

      public String toString()
      Overrides:
      toString in class Object