Crate bigtools

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 (BedParserStreamingIterator and BedParserParallelStreamingIterator) process incoming bed-like data and process into bigWig and bigBed files.
• utils

Structs

• BBIFileInfo
  Info on a bbi file
• BBIHeader
  Header info for a bbi file
• BBIWriteOptions
  Options for writing to a bbi file
• BedEntry
  Represents a single entry in a bigBed file
• BigBedRead
  The struct used to read a bigBed file
• BigBedWrite
  The struct used to write a bigBed file
• BigWigRead
  The struct used to read a bigWig file
• BigWigWrite
  The struct used to write a bigWig file
• Block
• CachedBBIFileRead
• ChromInfo
  Information on a chromosome in a bbi file
• CirTreeIndex
  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 to search_cir_tree.
• ReductionLevelNotFound
• Summary
  A summary of a section of data (may be an entire file)
• Value
  Represents a single value in a bigWig file
• ZoomHeader
  Info on a specific zoom level in a bbi file
• ZoomRecord
  A single zoom item

Enums

• BBIFile
  The type of bbi file
• BBIProcessError
  Possible errors encountered when processing a chromosome when writing a bbi file
• BBIReadError
  Possible errors encountered when reading a bbi file
• BigBedReadOpenError
  Possible errors encountered when opening a bigBed file to read
• BigWigReadOpenError
  Possible errors encountered when opening a bigWig file to read
• CirTreeIndexType
  What kind of cir tree in a bbi file
• CirTreeSearchError
• GenericBBIFileOpenError
  Possible errors encountered when opening a bigBed file to read
• GenericBBIRead
• InputSortType
  Options for required input sort order of values
• ProcessDataError
  Possible errors encountered when processing a value to a BBI file.
• ZoomIntervalError
  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

• BBIDataProcessor
• BBIDataSource
  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.
• BBIFileRead
• BBIRead
  Generic methods for reading a bbi file