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@lbergelson lbergelson released this 28 Sep 21:17
· 428 commits to master since this release
2.12.0
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lbergelson Louis Bergelson
GPG key ID: CDB73EA73CD9CF1E
Learn about vigilant mode.
86a7417

Notable changes:

  • expanded Path support to SamFileWriterFactory
  • upgraded Snappy to version 1.1.4, this brings us to using standard modern snappy rather than an ancient and unsupported beta version
  • support for writing VCFs records without outputting a header first
  • minor API additions, SAMRecord.hasAttribute(), new default methods on Locatable
  • additional tests and bug fixes

Deprecations:

These will be removed in a future release

  • StringLineReader in favor of a BufferedLineReader.fromString()
  • SortingVariantContextWriter and related classes, no replacement
  • FixBAMFile, no replacement

Breaking Changes:

  • new method VariantContextWriter.setHeader() must be provided by implementations, see the javadoc for more details, this should hopefully be an easy fix for most downstream users
  • removed main method from TabixReader

Complete change list:

86a7417 add default methods to Locatable (#443)
a35b420 Don't generate interrupt on close in AbstractAsyncWriter. (#992)
934fb62 Fix unhelpful exception message in IndexFactory (#987)
9b0bb26 renaming VariantContextWriter.setVCFHeader -> setHeader (#989)
b16ad36 Add convenience method hasAttibute() to SAMRecord (#963)
f0ff130 minor updates to snappy code (#983)
1e2ebd5 deprecating SortingVariantContextWriter (#982)
aa2d24a remove unnecessary array copy in TabixReader(#932)
fc9f2c4 Upgraded snappy-java to 1.1.4 #666 (#872)
9991e55 allow writing vcf records without writing a header #902 (#904)
04b17d5 Optimize intervals fails to merge abutting intervals #971 (#979)
4c5620b Simplify and deprecate StringLineReader (#974)
a0e38a9 Simplify BufferedLineReader by using LineNumberReader (#953)
1ade6c9 add Path options for SAMFileWriterFactory (#840)
e110f44 Increase coverage for SAMRecord query comparators (#948)
958dc6e Increase test coverage for SAMReadGroupRecord (#951)
4f4c505 cleaning up constructors in ReferenceSource (#970)
dcff7f5 Deprecate FixBAMFile.java (#947)
d5af563 speed up performance when creating a VCF header with a large number of contigs.
#934 (#968)

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