Public Member Functions
bool	output_id () const

bool	output_bx () const

bool	output_seq () const

bool	output_qual () const

bool	filter_in () const

bool	filter_out () const

bool	short_mode () const

bool	long_mode () const

Record	read ()

	Indexlr (std::string seqfile, size_t k, size_t w, unsigned flags=0, unsigned threads=5, bool verbose=false, const btllib::BloomFilter &bf1=Indexlr::dummy_bf(), const btllib::BloomFilter &bf2=Indexlr::dummy_bf())

	Indexlr (std::string seqfile, size_t k, size_t w, size_t q, unsigned flags=0, unsigned threads=5, bool verbose=false, const btllib::BloomFilter &bf1=Indexlr::dummy_bf(), const btllib::BloomFilter &bf2=Indexlr::dummy_bf())

void	close () noexcept

RecordIterator	begin ()

RecordIterator	end ()

Constructor & Destructor Documentation

◆ Indexlr()

inline

Construct Indexlr to calculate minimizers from sequences at the given path.

Parameters

seqfile	Filepath to read sequences from. Pass "-" to read from stdin.
k	k-mer size for the minimizer.
w	window size when selecting minimizers.
q	quality threshold to ignore potential minimizers.
flags	Modifier flags. Specifiying either short or long mode flag is mandatory; other flags are optional.
threads	Maximum number of processing threads to use. Must be at least 1.
verbose	Whether to output informational messages during processing.
bf1	A Bloom filter to use for either filtering minimizers in or out, if one of the flags is enabled. If both are enabled, bf1 is used for filtering in.
bf2	A second Bloom filter to use when both filtering minimizers in and out is enabled. bf2 is used for filtering out.

RecordIterator btllib::Indexlr::begin ( )

inline

For range-based for loop only.

Indexlr::Record btllib::Indexlr::read ( )

inline

Read the next Indexlr record, containing read information and a list of minimizers.

The documentation for this class was generated from the following file: