Expand description
Bigtools provides a high-level, performant API for reading and writing bigWig and bigBed files.
The original file format specification for bigWig and bigBed files is defined in this paper: https://doi.org/10.1093/bioinformatics/btq351
§Reading
The entrypoint to reading bigWigs and bigBeds is BigWigRead::open and
BigBedRead::open, respectively. These take any type that implements both
Read and Seek. There are also
BigWigRead::open_file and BigBedRead::open_file, which take a &str and
will open a File.
Once a BigWigRead or BigBedRead have been constructed, they can be read
in a number of ways. First, the info (in the form of BBIFileInfo) is available
in info fields. However, to access the main data, the most common method to call
is BigWigRead::get_interval or BigBedRead::get_interval, which returns an
Iterator of Values or BedEntrys overlapping the provided region, respectively.
§Writing
Writing new bigWigs and bigBeds is a tad more difficult. To begin, a
BigWigWrite or BigBedWrite can be created using
BigWigWrite::create_file or BigBedWrite::create_file.
Generally, bigWig and bigBed writing is done per chromosome, with compression and io being done on an async Runtime.
The source for data to be written to bigWigs and bigBeds come from the
BBIDataSource trait. It is used to abstracts over processing the data
for a bbi file. It is a lower-level API that can be useful for custom value
generation or scheduling logic. Generally though, users should not need to
implement this directly, but rather use provided structs BedParserStreamingIterator
and BedParserParallelStreamingIterator
types providing serial processing of a bed-like value stream (either from a
file or an iterator) or concurrent processing from a file. See the documentation on the trait for more
detailed information on how to implement.
Given some implementation of BBIDataSource (like BedParserStreamingIterator),
a bigWig can be created using BigWigWrite::write or a bigBed with
BigBedWrite::write. Both take a map of chromosome sizes, the aforementioned
data, and a Runtime to spawn processing on.
Modules§
- bed
- Contains utilities useful for reading and writing bed files and bed-like data.
- beddata
- The types here (
BedParserStreamingIteratorandBedParserParallelStreamingIterator) process incoming bed-like data and process into bigWig and bigBed files. - utils
Structs§
- BBIFile
Info - Info on a bbi file
- BBIHeader
- Header info for a bbi file
- BBIWrite
Options - Options for writing to a bbi file
- BedEntry
- Represents a single entry in a bigBed file
- BigBed
Interval Iter - BigBed
Read - The struct used to read a bigBed file
- BigBed
Write - The struct used to write a bigBed file
- BigWig
Interval Iter - BigWig
Read - The struct used to read a bigWig file
- BigWig
Write - The struct used to write a bigWig file
- Block
- CachedBBI
File Read - Chrom
Info - Information on a chromosome in a bbi file
- CirTree
Index - Represents a cir tree index in a bbi file. Composed of a public
CirTreeIndexType, and a private location in the bbi file. This can be passed tosearch_cir_tree. - Reduction
Level NotFound - Summary
- A summary of a section of data (may be an entire file)
- Value
- Represents a single value in a bigWig file
- Zoom
Header - Info on a specific zoom level in a bbi file
- Zoom
Interval Iter - Zoom
Record - A single zoom item
Enums§
- BBIFile
- The type of bbi file
- BBIProcess
Error - Possible errors encountered when processing a chromosome when writing a bbi file
- BBIRead
Error - Possible errors encountered when reading a bbi file
- BigBed
Read Open Error - Possible errors encountered when opening a bigBed file to read
- BigWig
Read Open Error - Possible errors encountered when opening a bigWig file to read
- CirTree
Index Type - What kind of cir tree in a bbi file
- CirTree
Search Error - GenericBBI
File Open Error - Possible errors encountered when opening a bigBed file to read
- GenericBBI
Read - Input
Sort Type - Options for required input sort order of values
- Process
Data Error - Possible errors encountered when processing a value to a BBI file.
- Zoom
Interval Error - Potential errors found when trying to read data from a zoom level
Constants§
- DEFAULT_
BLOCK_ SIZE - The default block size used when writing a bbi file
- DEFAULT_
ITEMS_ PER_ SLOT - The default items per slot used when writing a bbi file
Traits§
- BBIData
Processor - BBIData
Source - This trait abstracts over processing the data for a bbi file. Generally,
users should not need to implement this directly, but rather use provided
structs like
BedParserStreamingIterator. However, this does provide a lower-level API that can be useful for custom value generation or scheduling logic. - BBIFile
Read - BBIRead
- Generic methods for reading a bbi file