ReadHit Struct Reference

The ReadHit struct stores information for a single read alignment. More...

#include <fragments.h>

List of all members.

Public Attributes
std::string	name
	A public string for the SAM "Query Template Name" (fragment name)
bool	first
	A public bool specifying if this read was sequenced first according to the SAM flag.
bool	reversed
	A public bool specifying if this read was reverse complemented in its alignment according to the SAM flag.
size_t	targ_id
	A public TargID for the target mapped to.
size_t	left
	A public size_t containing the 0-based leftmost coordinate mapped to in the target.
size_t	right
	A public size_t containing the position following the 0-based rightmost coordinate mapped to in the target.
SequenceFwd	seq
	The read sequence.
std::vector< Indel >	inserts
	A public vector of Indel objects storing all insertions to the reference in the read.
std::vector< Indel >	deletes
	A public vector of Indel objects storing all insertions to the reference in the read.
BamTools::BamAlignment	bam
	A public BamAlignment object storing the raw alignment information from BamTools for the read.
std::string	sam
	A public string storing the raw alignment information from for the read.
int	mate_l
	A public int containing the left position for the mate of the read.

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Detailed Description

The ReadHit struct stores information for a single read alignment.

Author:

Adam Roberts

Date:

2012 Artistic License 2.0

Definition at line 63 of file fragments.h.

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Member Data Documentation

BamTools::BamAlignment ReadHit::bam

A public BamAlignment object storing the raw alignment information from BamTools for the read.

Only valid if BAM file is input.

Definition at line 111 of file fragments.h.

std::vector<Indel> ReadHit::deletes

A public vector of Indel objects storing all insertions to the reference in the read.

Deletions are stored in read order.

Definition at line 106 of file fragments.h.

std::vector<Indel> ReadHit::inserts

A public vector of Indel objects storing all insertions to the reference in the read.

Insertions are stored in read order.

Definition at line 101 of file fragments.h.

int ReadHit::mate_l

A public int containing the left position for the mate of the read.

-1 if single-end fragment. This is temporarily used to help find the mate but is not used after.

Definition at line 122 of file fragments.h.

bool ReadHit::reversed

A public bool specifying if this read was reverse complemented in its alignment according to the SAM flag.

This would also imply that the read is the left end of the fragment.

Definition at line 78 of file fragments.h.

std::string ReadHit::sam

A public string storing the raw alignment information from for the read.

Only valid if SAM file is input.

Definition at line 116 of file fragments.h.

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

• src/fragments.h