Function
readRecord
reads one record (e.g. a single DNA-sequence and its meta data) from a StreamConcept, by the means of RecordReader
readRecord(<format specific>, TRecordReader & reader, TTag const &)
readRecord(headerRecord, context, recordReader, tag)
readRecord(alignmentRecord, context, recordReader, tag)
readRecord(headerRecord, context, stream, tag)
readRecord(alignmentRecord, context, stream, tag)
readRecord(TIdString & meta, TSeqString & seq, TRecordReader & reader, Fasta const &)
readRecord(TIdString & meta, TSeqString & seq, TRecordReader & reader, Fastq const &)
readRecord(TIdString & meta, TSeqString & seq, TQualString & qual, TRecordReader & reader, Fastq const &)
Include Headers
seqan/bam_io.h, seqan/stream.h
Parameters
possibly multiple fields (e.g. meta and sequence)
reader
The reader object to read from
TTag
The file format tag
recordReader
The RecordReader to read from.
Remarks: Use for SAM.
header
BamHeader to read information into.
Types: BamHeader
context
The context to use for reading.
stream
The stream to read from (for BAM).
Remarks: BAM data can be read from any stream. For the proper decompression (from compressed BAM, the default) use BGZF Stream.
tag
Format to read BamHeader from.
Types: Bam, Sam
alignmentRecord
Remarks
If not noted otherwise, only a Single-Pass implementation is available for a the given format
For FASTA-Files a double-Pass implementation of RecordReader is implemented, which offers better performance. Just pass a Double-Pass reader object (only works with seekable Streams).
For FASTQ-Files a double-Pass implementation of RecordReader is implemented, which offers better performance. Just pass a Double-Pass reader object (only works with seekable Streams).
Member of
See Also
SeqAn - Sequence Analysis Library - www.seqan.de
 

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