View Source Bio.IO.FastQ (bio_elixir v0.2.0)
Allow the input/output of FASTQ formatted files.
This implementation references the documentation from NCBI and uses the Phred scoring 33 offset by default.
Link to this section Summary
Functions
Read a FASTQ formatted file into memory
Link to this section Types
@type quality_encoding() :: :phred_33 | :phred_64 | :decimal
@type read_opts() :: {:quality_encoding, quality_encoding()} | {:type, module()}
Link to this section Functions
@spec read(filename :: Path.t(), opts :: [read_opts()]) :: {:ok, [{struct(), struct()}]} | {:error, File.posix()}
Read a FASTQ formatted file into memory
Returns a list of tuples where the first struct is the type from the type
option, and the second is a Bio.IO.QualityScore struct.
options
Options
type- The module for the Sequence type that you want the returned value in. Defaults toBio.Sequence.DnaStrand. Module should implement theBio.Behaviours.Sequencebehaviour.quality_encoding- Determines the encoding of the quality scores.