Collaboration diagram for glfEntry:

Public Member Functions
glfEntry &	operator= (glfEntry &rhs)

Public Attributes
unsigned char	refBase:4
	"XACMGRSVTWYHKDBN"[ref_base] gives the reference base

unsigned char	recordType:4

unsigned int	offset
	offset of this record from the previous one, in bases

unsigned	depth:24
	log10 minimum likelihood * 10 and the number of mapped reads

unsigned	minLLK:8

unsigned char	mapQuality
	root mean squared maximum mapping quality for overlapping reads

union {

unsigned char lk [10]
	log10 likelihood ratio * 10 for genotypes AA, AC, AG, AT, CC, CG, CT, GG, GT, TT More...

glfIndel indel

};

Detailed Description

Definition at line 42 of file glfHandler.h.

Member Function Documentation

◆ operator=()

glfEntry & glfEntry::operator= ( glfEntry & rhs )

Definition at line 287 of file glfHandler.cpp.

{
    refBase = rhs.refBase;
    recordType = rhs.recordType;
    offset = rhs.offset;
    mapQuality = rhs.mapQuality;
 
    for (int i = 0; i < 10; i++)
        lk[i] = rhs.lk[i];
 
    minLLK = rhs.minLLK;
    depth = rhs.depth;
 
    return * this;
}

Member Data Documentation

◆ depth

unsigned glfEntry::depth

log10 minimum likelihood * 10 and the number of mapped reads

Definition at line 51 of file glfHandler.h.

◆ indel

glfIndel glfEntry::indel

Definition at line 60 of file glfHandler.h.

◆ lk

unsigned char glfEntry::lk[10]

log10 likelihood ratio * 10 for genotypes AA, AC, AG, AT, CC, CG, CT, GG, GT, TT

Definition at line 59 of file glfHandler.h.

◆ mapQuality

unsigned char glfEntry::mapQuality

root mean squared maximum mapping quality for overlapping reads

Definition at line 54 of file glfHandler.h.

◆ minLLK

unsigned glfEntry::minLLK

Definition at line 51 of file glfHandler.h.

◆ offset

unsigned int glfEntry::offset

offset of this record from the previous one, in bases

Definition at line 48 of file glfHandler.h.

◆ recordType

unsigned char glfEntry::recordType

Definition at line 45 of file glfHandler.h.

◆ refBase

unsigned char glfEntry::refBase

"XACMGRSVTWYHKDBN"[ref_base] gives the reference base