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Add a flexible array member to the bam1_t struct to facilitate a BAM … #393

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Add a flexible array member to the bam1_t struct to facilitate a BAM … #393

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6 changes: 6 additions & 0 deletions htslib/sam.h
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Original file line number Diff line number Diff line change
Expand Up @@ -163,6 +163,7 @@ typedef struct {
@field l_data current length of bam1_t::data
@field m_data maximum length of bam1_t::data
@field data all variable-length data, concatenated; structure: qname-cigar-seq-qual-aux
@field fam_data flexible array member for contiguous-memory optimization

@discussion Notes:

Expand All @@ -171,6 +172,10 @@ typedef struct {
on reading or from CIGAR.
3. cigar data is encoded 4 bytes per CIGAR operation.
4. seq is nybble-encoded according to bam_nt16_table.
5. fam_data can be used to allow the variable-length data to exist in
the same contiguous memory as the rest of the bam1_t. In that case,
for compatibility the data member should point to fam_data, and
m_data set to a large value (e.g., INT_MAX).
*/
typedef struct {
bam1_core_t core;
Expand All @@ -179,6 +184,7 @@ typedef struct {
#ifndef BAM_NO_ID
uint64_t id;
#endif
uint8_t fam_data[];
} bam1_t;

/*! @function
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