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 ChromData trait. It’s effectively like a powerful Iterator of ChromData::Output values, which itself is like peekable Iterator of values (either Values or BedEntrys for bigWigs or bigBeds respectively) over a chromosome. The ChromData::advance method takes a function that the current chromosome and returns a Future that will asynchronously process chromosomal data. This data can be returned immediately from the advance method, or can be stored (with the correct implementation) to queue multiple chromosomes simulatenously. The BedParserStreamingIterator and BedParserParallelStreamingIterator types provide serial processing of a bed-like value stream (either from a file or an iterator) or concurrent processing from a file. Generally, these underlying details aren’t necessary unless implementing a new data source.

Given some implementation of ChromData (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.
• bedchromdata
  The types here (BedParserStreamingIterator and BedParserParallelStreamingIterator) ultimately wrap around the a BedParser to interface with bigWig and bigBed writing.
• 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
• ChromProcessingKey
  An opaque key to indicate an processing chromosome
• 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
• 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
• ChromDataState
  Potential states encountered when reading ChromData
• 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
• ProcessChromError
  Possible errors encountered when processing a chromosome when writing 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

• BBIFileRead
• BBIRead
  Generic methods for reading a bbi file
• ChromData
  Effectively like an Iterator of chromosome data