read2

Function

reads an entire document from a StreamConcept, by the means of RecordReader

read2(<format specific>, TRecordReader & reader, TTag const &)

read2(StringSet<TIdString, TIdSpec> & sequenceIds, StringSet<TSeqString, TSeqSpec> & sequences, RecordReader<TFile, DoublePass<TSpec> > & reader, Fasta const &)

read2(StringSet<TIdString, TIdSpec> & sequenceIds, StringSet<TSeqString, TSeqSpec> & sequences, RecordReader<TFile, DoublePass<TSpec> > & reader, Fastq const &)

read2(StringSet<TIdString, TIdSpec> & sequenceIds, StringSet<TSeqString, TSeqSpec> & sequences, StringSet<TQualString, TQualSpec> & qualities, RecordReader<TFile, DoublePass<TSpec> > & reader, Fastq const &)

Include Headers

seqan/stream.h

Parameters

	possibly multiple StringSets (e.g. of meta and sequences)
reader	The reader object to read from Types: RecordReader
TTag	The file format tag

Remarks

This is only supported for Double-Pass IO. If you cannot use Double-Pass IO (e.g. when you cannot seek on the stream), loop over readRecord instead.

If not noted otherwise an especially efficient version of the function is used if all StringSets are specialized as ConcatDirect -StringSets.

Status

Should be renamed to "read" once the old IO-Code is removed

Member of

RecordReader