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See:
Description
Interface Summary | |
---|---|
FastqReader | Reader for FASTQ formatted sequences. |
FastqWriter | Writer for FASTQ formatted sequences. |
ParseListener | Low-level event based parser callback. |
StreamListener | Event based parser callback. |
Class Summary | |
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Fastq | FASTQ formatted sequence. |
FastqBuilder | Fluent builder API for creating FASTQ formatted sequences. |
FastqTools | Utility methods for FASTQ formatted sequences. |
IlluminaFastqReader | Reader for FastqVariant.FASTQ_ILLUMINA formatted sequences. |
IlluminaFastqWriter | Writer for FastqVariant.FASTQ_ILLUMINA formatted sequences. |
SangerFastqReader | Reader for FastqVariant.FASTQ_SANGER formatted sequences. |
SangerFastqWriter | Writer for FastqVariant.FASTQ_SANGER formatted sequences. |
SolexaFastqReader | Reader for FastqVariant.FASTQ_SOLEXA formatted sequences. |
SolexaFastqWriter | Writer for FastqVariant.FASTQ_SOLEXA formatted sequences. |
Enum Summary | |
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FastqVariant | FASTQ sequence format variant. |
FASTQ and variants sequence format I/O.
To read from an Illumina variant FASTQ sequence file:
FastqReader reader = new IlluminaFastqReader(); for (Fastq fastq : reader.read(new File("illumina.fastq")) { // ... }
To write to an 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
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