1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
|
..
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
Copyright (C) 2015 The Regents of the University of California.
It is licensed under the three-clause BSD license; see LICENSE.
Contact: khmer-project@idyll.org
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above
copyright notice, this list of conditions and the following
disclaimer in the documentation and/or other materials provided
with the distribution.
* Neither the name of the Michigan State University nor the names
of its contributors may be used to endorse or promote products
derived from this software without specific prior written
permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Contact: khmer-project@idyll.org
khmer/Oxli Binary File Formats
==============================
- 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.
khmer v1.4 and previous
~~~~~~~~~~~~~~~~~~~~~~~
CountingHash
------------
The header is in the format below, in file offset order. There is no magic
string.
================== =========== ==============================================
Field Length Value
================== =========== ==============================================
Version 1 ``0x04`` (``SAVED_FORMAT_VERSION``)
File Type 1 ``0x01`` (``SAVED_COUNTING_HT``)
Use Bigcount 1 ``1`` if bigcounts is used, else ``0``
K-size 1 k-mer length, ``1 <= k <= 32``
Number of Tables 1 Number of Count-min Sketch tables
================== =========== ==============================================
khmer v2.0 formats
~~~~~~~~~~~~~~~~~~
Magic string
------------
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.
Countgraph
----------
(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 ``OXLI`` (``SAVED_SIGNATURE``)
Version 1 4 ``0x04`` (``SAVED_FORMAT_VERSION``)
File Type 1 5 ``0x01`` (``SAVED_COUNTING_HT``)
Use Bigcount 1 6 ``0x01`` if bigcounts is used, else ``0x00``
K-size 4 7 k-mer length, ``ht._ksize``. [``uint32_t``]
Number of Tables 1 11 Number of Count-min Sketch tables,
``ht._n_tables``. [``uint8_t``]
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, ``ht._tablesizes[i]``.
[``uint64_t``]
Bins N 8 This table's bins, length given by previous
field. [``uint8_t``]
================== ===== ===== ==============================================
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 [``HashIntoType/uint64_t``].
Count 2 8 Kmer's count [``uint16_t``].
================== ===== ===== ==============================================
Nodegraph
---------
(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 ``OXLI`` (``SAVED_SIGNATURE``)
Version 1 4 ``0x04`` (``SAVED_FORMAT_VERSION``)
File Type 1 5 ``0x02`` (``SAVED_HASHBITS``)
K-size 4 6 k-mer length, ``ht._ksize``. [``unsigned int``]
Number of Tables 1 10 Number of Nodegraph tables. ``ht._n_tables``.
[``uint8_t``]
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** (``uint64_t``).
Bins N/8+1 8 This table's bytes, length given by previous
field, divided by 8, plus 1 (``uint8_t``).
================== ======= ===== ==============================================
.. todo:: Document ``Tags``, ``Stoptags``, ``Subset``, ``Labelset``
|
