├── requirements.txt
├── tests
    ├── test_input_1_a.bam.bai
    ├── test_input_1_b.bam.bai
    ├── test_input_1_c.bam.bai
    └── bai_indexer_test.py
├── .travis.yml
├── .gitignore
├── setup.py
├── README.md
├── bai_indexer
    └── __init__.py
└── LICENSE


/requirements.txt:
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1 | nose
2 | 


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/tests/test_input_1_a.bam.bai:
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https://raw.githubusercontent.com/hammerlab/bai-indexer/HEAD/tests/test_input_1_a.bam.bai


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/tests/test_input_1_b.bam.bai:
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https://raw.githubusercontent.com/hammerlab/bai-indexer/HEAD/tests/test_input_1_b.bam.bai


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/tests/test_input_1_c.bam.bai:
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https://raw.githubusercontent.com/hammerlab/bai-indexer/HEAD/tests/test_input_1_c.bam.bai


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/.travis.yml:
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1 | language: python
2 | python:
3 |   - "2.7"
4 | 
5 | install: "pip install -r requirements.txt"
6 | script: nosetests
7 | 


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/.gitignore:
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 1 | # Byte-compiled / optimized / DLL files
 2 | __pycache__/
 3 | *.py[cod]
 4 | 
 5 | # C extensions
 6 | *.so
 7 | 
 8 | # Distribution / packaging
 9 | .Python
10 | env/
11 | build/
12 | develop-eggs/
13 | dist/
14 | downloads/
15 | eggs/
16 | lib/
17 | lib64/
18 | parts/
19 | sdist/
20 | var/
21 | *.egg-info/
22 | .installed.cfg
23 | *.egg
24 | 
25 | # PyInstaller
26 | #  Usually these files are written by a python script from a template
27 | #  before PyInstaller builds the exe, so as to inject date/other infos into it.
28 | *.manifest
29 | *.spec
30 | 
31 | # Installer logs
32 | pip-log.txt
33 | pip-delete-this-directory.txt
34 | 
35 | # Unit test / coverage reports
36 | htmlcov/
37 | .tox/
38 | .coverage
39 | .cache
40 | nosetests.xml
41 | coverage.xml
42 | 
43 | # Translations
44 | *.mo
45 | *.pot
46 | 
47 | # Django stuff:
48 | *.log
49 | 
50 | # Sphinx documentation
51 | docs/_build/
52 | 
53 | # PyBuilder
54 | target/
55 | 


--------------------------------------------------------------------------------
/setup.py:
--------------------------------------------------------------------------------
 1 | from setuptools import setup, find_packages
 2 | 
 3 | try:
 4 |    import pypandoc
 5 |    description = pypandoc.convert('README.md', 'rst')
 6 | except (IOError, ImportError):
 7 |    description = ''
 8 | 
 9 | setup(name='bai-indexer',
10 |       version='0.1.1',
11 |       description='An index for your BAM Index (BAI)',
12 |       long_description=description,
13 |       author='Dan Vanderkam',
14 |       author_email='danvdk@gmail.com',
15 |       url='https://github.com/hammerlab/bai-indexer/',
16 |       entry_points={
17 |           'console_scripts': [
18 |               'bai-indexer = bai_indexer:run',
19 |           ],
20 |       },
21 |       packages=find_packages(exclude=['tests*']),
22 |       install_requires=[],
23 |       classifiers=[
24 |           'Environment :: Console',
25 |           'Development Status :: 4 - Beta',
26 |           'Intended Audience :: Healthcare Industry',
27 |           'Intended Audience :: Information Technology',
28 |           'License :: OSI Approved :: Apache Software License',
29 |           'Topic :: Scientific/Engineering :: Bio-Informatics'
30 |       ],
31 | )
32 | 


--------------------------------------------------------------------------------
/tests/bai_indexer_test.py:
--------------------------------------------------------------------------------
 1 | from nose.tools import *
 2 | 
 3 | from bai_indexer import index_stream
 4 | 
 5 | import StringIO
 6 | 
 7 | 
 8 | def test_file_a():
 9 |     eq_({
10 |             'chunks': [(8, 88), (88, 168), (168, 248), (248, 256)],
11 |             'minBlockIndex': 217
12 |         }, index_stream(open('tests/test_input_1_a.bam.bai')))
13 | 
14 | 
15 | def test_file_b():
16 |     eq_({
17 |             'chunks': [(8, 16), (16, 96), (96, 176), (176, 184)],
18 |             'minBlockIndex': 224
19 |         }, index_stream(open('tests/test_input_1_b.bam.bai')))
20 | 
21 | 
22 | def test_file_c():
23 |     eq_({
24 |             'chunks': [(8, 88), (88, 168)],
25 |             'minBlockIndex': 177
26 |         }, index_stream(open('tests/test_input_1_c.bam.bai')))
27 | 
28 | 
29 | def test_stdin():
30 |     # sys.stdin only has a read() method.
31 |     stream = open('tests/test_input_1_c.bam.bai')
32 |     class FakeStdin(object):
33 |         read = stream.read
34 | 
35 |     eq_({
36 |             'chunks': [(8, 88), (88, 168)],
37 |             'minBlockIndex': 177
38 |         }, index_stream(FakeStdin()))
39 | 


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/README.md:
--------------------------------------------------------------------------------
 1 | [![Build Status](https://travis-ci.org/hammerlab/bai-indexer.svg?branch=master)](https://travis-ci.org/hammerlab/bai-indexer)
 2 | 
 3 | bai-indexer
 4 | ===========
 5 | 
 6 | Build an index for your BAM Index (BAI).
 7 | 
 8 | Background
 9 | ----------
10 | 
11 | [BAM][1] is a common file format for storing aligned reads from a gene
12 | sequencing machine. These files can get enormous (100+ GB), so it's helpful to
13 | have an index to support fast lookup.
14 | 
15 | [Samtools][2] defines a file format for a BAM index and provides a simple
16 | command for generating one:
17 | 
18 | ```
19 | samtools index file.bam file.bam.bai
20 | ```
21 | 
22 | Unfortunately, these BAM Index (BAI) files can _also_ grow very large, often to
23 | 10 MB or more. When using a genome browser like [IGV][3] or [BioDalliance][4],
24 | loading a large BAI file over a slow network is the unavoidable first step in
25 | displaying alignment tracks.
26 | 
27 | bai-indexer solves this problem by building an index of your BAM Index. This is
28 | a small JSON file which maps reference ID (i.e. chromosome number) to a byte
29 | range within the BAI file. By loading the BAM index, a viewer can load only the
30 | small subset of the BAM index that it actually needs.
31 | 
32 | Usage
33 | -----
34 | 
35 |     pip install bai-indexer
36 | 
37 |     bai-indexer path/to/file.bam.bai > path/to/file.bam.bai.json
38 | 
39 | Format
40 | ------
41 | 
42 | The JSON index index looks like this:
43 | 
44 | ```json
45 | {
46 |   "chunks": [
47 |     [8, 716520],
48 |     [716520, 1463832],
49 |     [1463832, 2070072],
50 |     ...
51 |   ],
52 |   "minBlockIndex": 1234
53 | }
54 | ```
55 | 
56 | The first chunk (`[8, 716520]`) specifies the byte range in the BAI file which
57 | describes the first ref (most likely `chr1` for a human genome). This is a
58 | half-open `[start, stop)` interval.
59 | 
60 | The `minBlockIndex` field specifies the position of the first block in the BAM
61 | file. Everything before this position is headers.
62 | 
63 | Development
64 | -----------
65 | 
66 | After setting up a virtualenv, you can get going by running:
67 | 
68 | ```bash
69 | pip install -r requirements.txt
70 | nosetests
71 | ```
72 | 
73 | 
74 | [1]: https://github.com/samtools/hts-specs
75 | [2]: http://www.htslib.org/
76 | [3]: http://www.broadinstitute.org/igv/
77 | [4]: http://www.biodalliance.org/
78 | 


--------------------------------------------------------------------------------
/bai_indexer/__init__.py:
--------------------------------------------------------------------------------
  1 | #!/usr/bin/env python
  2 | """Print out start:stop locations for each reference in a BAI file.
  3 | 
  4 | Usage:
  5 |     bai_indexer.py /path/to/file.bam.bai > /path/to/file.bam.bai.json
  6 | """
  7 | 
  8 | import json
  9 | import struct
 10 | import sys
 11 | 
 12 | # -- helper functions for reading binary data from a stream --
 13 | 
 14 | def _unpack(stream, fmt):
 15 |     size = struct.calcsize(fmt)
 16 |     buf = stream.read(size)
 17 |     return struct.unpack(fmt, buf)[0]
 18 | 
 19 | 
 20 | def _read_int32(stream):
 21 |     return _unpack(stream, '<i')
 22 | 
 23 | 
 24 | def _read_uint32(stream):
 25 |     return _unpack(stream, '<I')
 26 | 
 27 | 
 28 | def _read_uint64(stream):
 29 |     return _unpack(stream, '<Q')
 30 | 
 31 | 
 32 | class _TellingStream(object):
 33 |     """Wrapper for a stream which adds support for tell(), e.g. to stdin."""
 34 |     def __init__(self, stream):
 35 |         self._stream = stream
 36 |         self._pos = 0
 37 | 
 38 |     def read(self, *args):
 39 |         data = self._stream.read(*args)
 40 |         self._pos += len(data)
 41 |         return data
 42 | 
 43 |     def tell(self):
 44 |         return self._pos
 45 | 
 46 | 
 47 | class InvalidBaiFileError(Exception):
 48 |     pass
 49 | 
 50 | 
 51 | def index_stream(bai_stream):
 52 |     """Generate an index of a BAM Index (BAI) file.
 53 | 
 54 |     Args:
 55 |         data_stream: A stream of bytes from the BAI file, as returned
 56 |             by open().  Anything with a .read() method will do.
 57 | 
 58 |     Returns:
 59 |         A dict with information about the BAM and BAI files. For example:
 60 | 
 61 |         {'minBlockIndex': 1234,
 62 |          'chunks': [[8, 123456], [123456, 234567], ...]}
 63 | 
 64 |         The chunks are [start, stop) byte ranges in the BAI file for each
 65 |         ref. minBlockIndex is the position of the first block in the BAM
 66 |         file.
 67 | 
 68 |     Raises:
 69 |         InvalidBaiFileError: if the bytes do not comprise a valid BAI file.
 70 |     """
 71 |     data_stream = _TellingStream(bai_stream)
 72 | 
 73 |     # The logic and naming below follow the diagram on page 16 of
 74 |     # http://samtools.github.io/hts-specs/SAMv1.pdf
 75 |     magic = data_stream.read(4)
 76 |     if magic != 'BAI\x01':
 77 |         raise InvalidBaiFileError('This is not a BAI file (missing magic)')
 78 | 
 79 |     minBlockIndex = 1000000000
 80 |     refs = []
 81 |     n_ref = _read_int32(data_stream)
 82 |     for i in range(0, n_ref):
 83 |         ref_start = data_stream.tell()
 84 |         n_bin = _read_int32(data_stream)
 85 |         for j in range(0, n_bin):
 86 |             bin_id = _read_uint32(data_stream)
 87 |             n_chunk = _read_int32(data_stream)
 88 | 
 89 |             chunks = []
 90 |             for k in range(0, n_chunk):
 91 |                 chunk_beg = _read_uint64(data_stream)
 92 |                 chunk_end = _read_uint64(data_stream)
 93 | 
 94 |         n_intv = _read_int32(data_stream)
 95 |         intvs = []
 96 |         for j in range(0, n_intv):
 97 |             ioffset = _read_uint64(data_stream)
 98 |             if ioffset:
 99 |                 # These values are "virtual offsets". The first 48 bits are the
100 |                 # offset of the start of the compression block in the BAM file.
101 |                 # The remaining 16 bits are an offset into the inflated block.
102 |                 bi = ioffset / 65536
103 |                 if ioffset % 65536 != 0:
104 |                     bi += 65536
105 |                 minBlockIndex = min(minBlockIndex, bi)
106 |         ref_end = data_stream.tell()
107 | 
108 |         refs.append((ref_start, ref_end))
109 | 
110 |     # Undocumented field: # of unmapped reads
111 |     # See https://github.com/samtools/hts-specs/pull/2/files
112 |     try:
113 |         num_unmapped = _read_uint64(data_stream)
114 |     except struct.error:
115 |         pass
116 | 
117 |     extra_bytes = data_stream.read()
118 |     if extra_bytes != '':
119 |         raise InvalidBaiFileError(
120 |                 'Extra data after expected EOF (%d bytes)' % len(extra_bytes))
121 | 
122 |     return {
123 |         'minBlockIndex': minBlockIndex,
124 |         'chunks': refs
125 |     }
126 | 
127 | 
128 | def run():
129 |     if len(sys.argv) != 2:
130 |         sys.stderr.write(__doc__)
131 |         sys.exit(1)
132 | 
133 |     if sys.argv[1] == '-':
134 |         sys.argv[1] = '/dev/stdin'
135 |     data = open(sys.argv[1], 'rb')
136 |     out = index_stream(data)
137 |     print json.dumps(out)
138 | 
139 | 
140 | if __name__ == '__main__':
141 |     run()
142 | 


--------------------------------------------------------------------------------
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