0.8.0

Version 0.8.0

Released on April 29th 2018

New

• HTTP/HTTPS urls support for BigWig, BigBed, TDF files. Server is
  supposed to support accept-ranges http header
• New buffer factories for files/urls reading based on hts-jdk
  SeekableStream:
  • Without concurrent BigFile access support: EndianBufferFactory
  • With concurrent BigFile access support: EndianSynchronizedBufferFactory,
    EndianThreadSafeBufferFactory
• Big files read and write methods accepts cancelledChecker closure to
  abort current operation, e.g. if you need to render another range.
  Just throw exception in this closure.
• 'BigFile#BigFile.determineFileType(src)' returns src file type, could be
  BigFile.Type.BIGBED, BigFile.Type.BIGWIG or null.

Changed

• Show 'Header extensions are unsupported' only in debug log
• Use RomBufferFactory to detect file endianness
• Changed prefetch option to int value in BigFile.read(),
  BigWigFile.read(), BigBedFile.read(). Supported values are:
  • BigFile.PREFETCH_LEVEL_OFF : do not prefetch
  • BigFile.PREFETCH_LEVEL_FAST : prefetch zoom level indexes tree,
    chromosomes list
  • BigFile.PREFETCH_LEVEL_DETAILED : prefetch w/o zoom level data tree
    indexes up to chromosomes level
    Larger prefetch values increase big file opening time and memory
    consumption but provides faster data access with fewer i/o operations

Removed:

• RandomAccessFile based factory and rom buffer
  removed. Please use EndianBufferFactory, EndianThreadSafeBufferFactory
  or EndianSynchronizedBufferFactory factories instead.