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@lbergelson lbergelson released this 12 May 17:03
· 668 commits to master since this release
2.3.0
67cdbc4

Bug fixes:

  • URIs to gzipped files that have trailing parameters are properly understood to be gzipped now

API Changes:

  • new CRAMReferenceSource interface has been extracted from ReferenceSource this enables users to provide custom cram reference sources
  • some methods that previously returned ReferenceSource now return CRAMReferenceSource this may be a breaking change for some downstream users who are doing work with cram

Complete change list:

  • c775754 Factor out an interface from CRAM ReferenceSource and fix two URI bugs.
  • 5e87478 adding a useAsynchronousIO flag to SamReaderFactory
  • 4a3fa96 fix setter in factory
  • b0054c5 Rename internal reg2bin method and make it public
  • d181e9e Document lack of support for BCF version 2.2
  • a2f8156 Addressed code review; fixed potential deadlock if background thread throw exception from hasNext() call
  • 9d21865 AsyncBufferedIterator implementation to improve throughput by performing read-ahead on a background thread

Thank you to community contributors @d-cameron, @lindenb, and @heuermh.

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