C++ macro definitions are given in parenthesis.
C++ types are given in square brackets.
Len
is the field’s size, in bytes, and Off
is the field’s zero-based
byte offset in the file/section.
The header is in the format below, in file offset order. There is no magic string.
Field |
Length |
Value |
---|---|---|
Version |
1 |
|
File Type |
1 |
|
Use Bigcount |
1 |
|
K-size |
1 |
k-mer length, |
Number of Tables |
1 |
Number of Count-min Sketch tables |
All formats shall have the “magic string” OXLI
as their first bytes, after
any external compression/encoding (e.g. gzip encapsulation) is removed. Note
that this makes them incompatible with older versions of khmer.
(a.k.a CountingHash
, a Count-min Sketch)
The header is in the format below, again in the order of file offset.
Field |
Len |
Off |
Value |
---|---|---|---|
Magic string |
4 |
0 |
|
Version |
1 |
4 |
|
File Type |
1 |
5 |
|
Use Bigcount |
1 |
6 |
|
K-size |
4 |
7 |
k-mer length, |
Number of Tables |
1 |
11 |
Number of Count-min Sketch tables,
|
Occupied Bins |
8 |
12 |
Number of occupied bins |
Then follows the Countgraph’s tables. For each table:
Field |
Len |
Off |
Value |
---|---|---|---|
Table size |
8 |
0 |
Length of this table, |
Bins |
N |
8 |
This table’s bins, length given by previous
field. [ |
Then follows a single value, the [uint64_t
] number of kmer: count
pairs. Then follows the Bigcount map, if this number is greater than zero. For
each kmer:
Field |
Len |
Off |
Value |
---|---|---|---|
Kmer |
8 |
0 |
Kmer’s hash [ |
Count |
2 |
8 |
Kmer’s count [ |
(a.k.a HashBits
, a Bloom Filter)
The header is in the format below, again in the order of file offset. Value macro definitions are given in parenthesis
Field |
Len |
Off |
Value |
---|---|---|---|
Magic string |
4 |
0 |
|
Version |
1 |
4 |
|
File Type |
1 |
5 |
|
K-size |
4 |
6 |
k-mer length, |
Number of Tables |
1 |
10 |
Number of Nodegraph tables. |
Occupied Bins |
8 |
11 |
Number of occupied bins |
Then follows the Nodegraph’s tables. For each table:
Field |
Len |
Off |
Value |
---|---|---|---|
Table size |
8 |
0 |
Length of table, in bits ( |
Bins |
N/8+1 |
8 |
This table’s bytes, length given by previous
field, divided by 8, plus 1 ( |