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@lbergelson lbergelson released this 02 Jan 21:23
· 395 commits to master since this release
2.14.0
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lbergelson Louis Bergelson
GPG key ID: CDB73EA73CD9CF1E
Learn about vigilant mode.
80122b9

This small release includes bug fixes and additional support for reading VCF's from java.nio.Path using VcfFileReader.

It was already possible to read VCFs from a Path with a more convoluted method, but VcfFileReader is a convenient way to do so.

BREAKING CHANGE:

  • new abstract method SamReaderFactory.getFileHeader(Path samFile)
    This should have no impact for most users unless you're providing custom implementations of SamReaderFactory. If you are, your subclasses will have to implement this new method.

Deprecations:

  • SAMSequenceDictionaryExtractor.extractDictionary(File) has been deprecated, use SAMSequenceDictionaryExtractor.extractDictionary(Path) instead

80122b9 Enable VcfFileReader and other classes to use Path (#1018)
335cd06 Modify FilterTag to Pass or Filter reads (#1052)
7ee6d55 Add checks on Histogram::getPercentile to protect against negative and zero values(#1043)
3308baf Strip query parameters from url before testing for block compressed extension #1021 (#1033)

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