FASTQ and variants sequence format I/O.

To read from an Illumina variant FASTQ sequence file:

 FastqReader reader = new IlluminaFastqReader();
 for (Fastq fastq : File("illumina.fastq"))
   // ...
To write to a Sanger variant FASTQ sequence file:
 Collection<Fastq> fastq = ...;
 SangerFastqWriter writer = new SangerFastqWriter();
 writer.write(new File("sanger.fastq"), fastq);
For further documentation on the FASTQ sequence format, its variants, and how they are handled in O|B|F projects, see:

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

Peter J. A. Cock (Biopython), Christopher J. Fields (BioPerl), Naohisa Goto (BioRuby), Michael L. Heuer (BioJava) and Peter M. Rice (EMBOSS).
Nucleic Acids Research, doi:10.1093/nar/gkp1137

Moved from org.biojava.nbio.sequencing (biojava-sequencing module) in 5.0.0