Alignment, e.g. map.list file entry. More...

Classes
struct	accessory
	Additional alignment information, usually represented as optional tags. More...

Public Types
enum	InsertState { PE_UNSPECIFIED, PE_FILTER_ORPHAN, PE_TECHNICAL, PE_PAIRED, PE_CONCORDANT, PE_DISCORDANT, PE_MAPPING_ORPHAN, PE_ACCESSORY, PE_SUBOPTIMAL }
	Translates PE flags into true for first read, false otherwise. More...

typedef bool(*	cmp_type )(const alignment &, const alignment &)
	Comparator type.

Public Member Functions
	alignment ()
	Constructor: set defaults.

char	get_qual_std_char (const size_t pos) const
	Get the quality char for a position (starting from the end of the quality string for reverse strand alignments).

char	get_qual_aux_char (const size_t pos) const
	Get the aux. quality char for a position (starting from the end of the quality string for reverse strand alignments).

int	get_qual_std (const size_t pos) const
	Get the integer quality value in range 0..40 for a position (starting from the end of the quality string for reverse strand alignments).

int	get_qual_aux (const size_t pos) const
	Get the aux. quality value in range 50..100 for a position (starting from the end of the quality string for reverse strand alignments).

bool	is_firstread () const
	Get pe flag without the library 'name space' information. More...

bool	is_lastread () const
	Second read of a PE run.

bool	is_fwd_frag () const
	Read1 and on the fwd strand or read2 and on the rev strand.

bool	is_rev_frag () const
	Read1 and on the rev strand or read2 and on the fwd strand.

bool	partner_mapped () const
	Test if the partner is mapped.

Static Public Member Functions
static bool	cmp_coor (const alignment &f1, const alignment &f2)
	Position comparator.

static bool	cmp_id (const alignment &f1, const alignment &f2)
	ID comparator.

static bool	cmp_null (const alignment &f1, const alignment &f2)
	Pseudo comparator, always returns false –> everything is equal.

Public Attributes
std::string	id
	ID of the fragment that the read comes from.

shore::refseq_coor	coor
	Reference sequence coordinates of the alignment.

size_t	readlength
	Length of the read.

shore::Strand	strand
	Strand.

int	hits
	Total number of mappings for the read corresponding to this alignment.

std::string	alignment_string
	Alignment string.

int	mismatches
	Edit distance / score for the alignment.

size_t	offset
	Query offset value for fully local alignments.

int	index
	Pairing information.

InsertState	pe_state

std::string	qual_std
	Quality string.

std::string	qual_aux
	Auxiliary quality string (default: chastity).

std::string	qual_raw
	Legacy quality string.

accessory	tags
	Optional information.

Static Public Attributes
static const char	strandconv_dp [5]
	Translates shore::STR_FWD and shore::STR_REV into 'D' and 'P'.

static const read::InsertState	insstate_flatten [9]

static const char	insstate_enc [10]

Detailed Description

Alignment, e.g. map.list file entry.

Member Enumeration Documentation

Translates PE flags into true for first read, false otherwise.

Paired end sequencing attributes.

Enumerator
PE_UNSPECIFIED	Any of the below.
PE_FILTER_ORPHAN	Partner lost due to quality filtering.
PE_TECHNICAL	E.g. barcode read.
PE_PAIRED	Not PE_FILTER_ORPHAN or PE_TECHNICAL, any of the below.
PE_CONCORDANT	Forms a likely pairing with it's partner, given the insert.
PE_DISCORDANT	Neither this mapping of the read, nor any other can participate in a likely pairing.
PE_ACCESSORY	Discordant, and another mapping of the read is concordant.

bool shore::alignment::is_firstread ( ) const

Get pe flag without the library 'name space' information.

Check if pe flag indicates the first read. First read of a PE or single end run.

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