gamgee::ReadGroup Class Reference

Helper struct to hold one read group record from a sam file header. More...

#include <read_group.h>

Public Member Functions
	ReadGroup ()=default
	ReadGroup (const std::string &header_line)
	creates and populates a read group object from a sam header line More...

Public Attributes
std::string	id
std::string	center
std::string	description
std::string	date_time
std::string	flow_order
std::string	key_sequence
std::string	library
std::string	programs
std::string	median_insert_size
std::string	platform
std::string	platform_unit
std::string	sample

Detailed Description

Helper struct to hold one read group record from a sam file header.

A read group, which is contained in a line starting with "@RG" in a sam file header, contains information about the seuencing process: type of machine, time, center etc. Most important for variant calling and quality control is the sample ID – each sample may be split into several read groups.

Constructor & Destructor Documentation

gamgee::ReadGroup::ReadGroup ( )

default

gamgee::ReadGroup::ReadGroup

(

const std::string &

header_line

)

creates and populates a read group object from a sam header line

Note

A read group line in a SAM header starts with "@RG" and then has tag/value pairs separated by whitespace. The tags are all length-2 strings and the tags are separated from values by colons. Ex: ID:12345.67 SM:11111 PL:Illumina

Member Data Documentation

std::string gamgee::ReadGroup::center

std::string gamgee::ReadGroup::date_time

std::string gamgee::ReadGroup::description

std::string gamgee::ReadGroup::flow_order

std::string gamgee::ReadGroup::id

std::string gamgee::ReadGroup::key_sequence

std::string gamgee::ReadGroup::library

std::string gamgee::ReadGroup::median_insert_size

std::string gamgee::ReadGroup::platform

std::string gamgee::ReadGroup::platform_unit

std::string gamgee::ReadGroup::programs

std::string gamgee::ReadGroup::sample

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

• gamgee/sam/read_group.h
• gamgee/sam/read_group.cpp