Range index class. More...

Classes
struct	build_spec
	Parameters for index creation. More...

struct	bytecount
	Helper for keeping track of the number of bytes read. More...

struct	header
	Index header record. More...

Public Types
enum	D2Type { D2_SIZE, D2_INCLUSIVE, D2_EXCLUSIVE, D2_MAPLIST, D2_CIGAR }

enum	QueryMode { QRY_OVERLAPPING, QRY_INCLUDING, QRY_INCLUDED }
	Mode of the query. More...

Public Member Functions
	twodex (const std::string &indexfile, const QueryMode qm=QRY_OVERLAPPING)
	Constructor, load an index file.

void	set_querymode (const QueryMode qm)

const header &	get_header () const

void	query (std::set< size_t > &res, const std::pair< long, long > &r) const

void	query (std::set< size_t > &res, const shore::genomic_range &r) const

std::pair< long, long >	range_enc (const shore::genomic_range &r) const

int	test (const shore::genomic_range &r1, const shore::genomic_range &r2) const

int	test (const shore::genomic_range &r1, const std::pair< long, long > &r2) const

Static Public Member Functions
static void	build (const std::string &fn, const std::string &colspec, const size_t blocksize, const size_t maxgap, const D2Type d2type, const char commentchar, std::ostream *const log=0)
	Create an index for a file. More...

static void	build (const std::string &fn, const build_spec &bs, std::ostream *const log=0)

static void	parse_xend (long *const xend, const long pos, const D2Type d2type, const std::string &d2, shore::alignment_helper &ah)
	Helper for getting the exclusive end position.

static int	test (const std::pair< long, long > &r1, const std::pair< long, long > &r2, const QueryMode querymode)
	test r1 vs r2 More...

Detailed Description

Range index class.

Member Enumeration Documentation

Mode of the query.

Enumerator
QRY_OVERLAPPING	Query for overlapping ranges.
QRY_INCLUDING	Query for ranges that include the query.
QRY_INCLUDED	Query for ranges that are included by the query.

static void shore::twodex::build	(	const std::string &	fn,
		const std::string &	colspec,
		const size_t	blocksize,
		const size_t	maxgap,
		const D2Type	d2type,
		const char	commentchar,
		std::ostream *const	log = `0`
	)

static

Create an index for a file.

Parameters

fn	Input file; the output file will be named <fn_without_compression_suffix>.2dex
colspec	Input file column specification: <seqname><position><end\|size\|...>
blocksize	Block size determining the index resolution in bytes.
maxgap	Maximum sequence gap allowed in a block.
d2type	Type of the second dimension of the range: end\|size\|...
commentchar	Character that indicates a comment line.
log	Log output stream pointer, may be nullptr.

static

test r1 vs r2

Returns: 0 match according to querymode; 1 no match, but matches to r2 may occur later in a sorted file; -1 no match, and no further matches to r2 if the file is sorted

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