The Tabix index file format

Field	Description	Type	Value
`magic`	Magic string	`char[4]`	TBI $\backslash$ 1
`n_ref`	# sequences	`int32_t`
`format`	Format (0: generic; 1: SAM; 2: VCF)	`int32_t`
`col_seq`	Column for the sequence name	`int32_t`
`col_beg`	Column for the start of a region	`int32_t`
`col_end`	Column for the end of a region	`int32_t`
`meta`	Leading character for comment lines	`int32_t`
`skip`	# lines to skip at the beginning	`int32_t`
`l_nm`	Length of concatenated sequence names	`int32_t`
`names`	Concatenated names, each zero terminated	`char[l_nm]`
List of indices (n=n_ref)
`n_bin`	# distinct bins (for the binning index)	`int32_t`
List of distinct bins (n=n_bin)
`bin`	Distinct bin number	`uint32_t`
`n_chunk`	# chunks	`int32_t`
List of chunks (n=n_chunk)
`cnk_beg`	Virtual file offset of the start of the chunk	`uint64_t`
`cnk_end`	Virtual file offset of the end of the chunk	`uint64_t`
`n_intv`	# 16kb intervals (for the linear index)	`int32_t`
List of distinct intervals (n=n_intv)
`ioff`	File offset of the first record in the interval	`uint64_t`
`n_no_coor` (optional)	# unmapped reads without coordinates set	`uint64_t`

Notes:

The index file is BGZF compressed.
All integers are little-endian.
When (format&0x10000) is true, the coordinate follows the BED rule (i.e. half-closed-half-open and zero based); otherwise, the coordinate follows the GFF rule (closed and one based).
For the SAM format, the end of a region equals POS plus the reference length in the alignment, inferred from CIGAR. For the VCF format, the end of a region equals POS plus the size of the deletion.
Field col_beg may equal col_end, and in this case, the end of a region is end=beg+1.
Example. For GFF, format=0, col_seq=1, col_beg=4, col_end=5, meta=‘#’ and skip=0. For BED, format=0x10000, col_seq=1, col_beg=2, col_end=3, meta=‘#’ and skip=0.

Given a zero-based, half-closed and half-open region [beg, end), the bin number is calculated with the following C function:

int reg2bin(int beg, int end) {
  --end;
  if (beg>>14 == end>>14) return ((1<<15)-1)/7 + (beg>>14);
  if (beg>>17 == end>>17) return ((1<<12)-1)/7 + (beg>>17);
  if (beg>>20 == end>>20) return  ((1<<9)-1)/7 + (beg>>20);
  if (beg>>23 == end>>23) return  ((1<<6)-1)/7 + (beg>>23);
  if (beg>>26 == end>>26) return  ((1<<3)-1)/7 + (beg>>26);
  return 0;
}

The list of bins that may overlap a region [beg, end) can be obtained with the following C function.

#define MAX_BIN (((1<<18)-1)/7)
int reg2bins(int rbeg, int rend, uint16_t list[MAX_BIN])
{
  int i = 0, k;
  --rend;
  list[i++] = 0;
  for (k =    1 + (rbeg>>26); k <=    1 + (rend>>26); ++k) list[i++] = k;
  for (k =    9 + (rbeg>>23); k <=    9 + (rend>>23); ++k) list[i++] = k;
  for (k =   73 + (rbeg>>20); k <=   73 + (rend>>20); ++k) list[i++] = k;
  for (k =  585 + (rbeg>>17); k <=  585 + (rend>>17); ++k) list[i++] = k;
  for (k = 4681 + (rbeg>>14); k <= 4681 + (rend>>14); ++k) list[i++] = k;
  return i; // #elements in list[]
}