The FastQ format. (tag) More...
#include <seqan3/io/sequence_file/format_fastq.hpp>
Static Public Attributes | |
static std::vector< std::string > | file_extensions |
The valid file extensions for this format; note that you can modify this value. More... | |
The FastQ format. (tag)
FastQ is the de-facto-standard for storing sequences together with quality information. See the article on wikipedia for a an in-depth description of the format.
The FastQ format provides the fields seqan3::field::SEQ, seqan3::field::ID and seqan3::field::QUAL; or alternatively provides seqan3::field::SEQ_QUAL as a single field of sequence and quality. All three fields (or ID + SEQ_QUAL) are required when writing and the sequence and qualities are required to be of the same length.
All documented encodings for the quality string are supported (see the article above), but they are not detected from the file. Instead, when reading the file, you have to set the respective alphabet via a traits type (see seqan3::SequenceFileInputTraits and the Quality submodule).
This implementation supports the following optional features of the format:
+
-line also (line is always ignored when reading)
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inlinestatic |
The valid file extensions for this format; note that you can modify this value.