Function
readRecord
reads one record (e.g. a single DNA-sequence and its meta data) from a Stream, by the means of RecordReader
Read Lastz "general" format record.
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 &)
readRecord(headerRecord, context, stream, tag)
readRecord(alignmentRecord, context, stream, tag)
readRecord(headerRecord, context, recordReader, tag)
readRecord(alignmentRecord, context, recordReader, tag)
readRecord(<format specific>, TRecordReader & reader, TTag const &)
readRecord(store, stream, StellarGff())
readRecord(store, stream, BlastnTabular())
readRecord(store, stream, LastzGeneral())
Include Headers
seqan/bam_io.h, seqan/parse_lm.h, seqan/stream.h
Parameters
header
BamHeader to read information into.
Types: BamHeader
context
The context to use for reading.
stream
The stream to read from (for BAM).
Types: Stream
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
recordReader
The RecordReader to read from.
Remarks: Use for SAM.
possibly multiple fields (e.g. meta and sequence)
reader
The reader object to read from
TTag
The file format tag
store
LocalMatchStore object to read into.
LocalMatchStore object to read into.
LocalMatchStore object to read into.
Remarks
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).
If not noted otherwise, only a Single-Pass implementation is available for a the given format
Return Values
int, 0 on success, non-0 on errors and EOF
int, 0 on success, non-0 on errors and EOF
int, 0 on success, non-0 on errors and EOF
See Also
SeqAn - Sequence Analysis Library - www.seqan.de
 

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