bam1_core_t

! @typedef @abstract Structure for core alignment information. @field tid chromosome ID, defined by bam_hdr_t @field pos 0-based leftmost coordinate @field bin bin calculated by bam_reg2bin() @field qual mapping quality @field l_qname length of the query name @field flag bitwise flag @field l_extranul length of extra NULs between qname & cigar (for alignment) @field n_cigar number of CIGAR operations @field l_qseq length of the query sequence (read) @field mtid chromosome ID of next read in template, defined by bam_hdr_t @field mpos 0-based leftmost coordinate of next read in template

Members

Variables

bin
uint16_t bin;

bin calculated by bam_reg2bin()

flag
uint16_t flag;

bitwise flag

isize
int32_t isize;

? template length

l_extranul
uint8_t l_extranul;

length of extra NULs between qname & cigar (for alignment)

l_qname
uint8_t l_qname;

length of the query name

l_qseq
int32_t l_qseq;

length of the query sequence (read)

mpos
int32_t mpos;

0-based leftmost coordinate of next read in template (mate)

mtid
int32_t mtid;

chromosome ID of next read in template, defined by bam_hdr_t

n_cigar
uint32_t n_cigar;

number of CIGAR operations

pos
int32_t pos;

0-based leftmost coordinate

qual
uint8_t qual;

mapping quality

tid
int32_t tid;

chromosome ID, defined by bam_hdr_t

unused1
uint8_t unused1;

padding

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