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@lbergelson lbergelson released this 16 Nov 22:23
· 271 commits to master since this release
2.18.0
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lbergelson Louis Bergelson
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Learn about vigilant mode.
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Learn about vigilant mode.

This is a smallish release with some new features. The biggest change is that bams created by htsjdk are now version 1.6. This should really have happened when started producing bams with long CIGAR support (CG tag) since that's the marquee 1.6 feature.

Compatibility:

This release is not backwards compatible with 2.17.0 but upgrading should be easy for most users.

Incompatible changes

  • Delete long deprecated FixBAMFile and SAMTools classes (#1213, #955, #972)
  • There continue to be major changes to the to htsjdk.samtools.cram package.

New Deprecations:

  • Deprecating SAMTagUtils, use SAMTag instead.
  • Deprecating tags in SAMTag that are deprecated in the SAM spec. These are deprecated to discourage use, but will not be removed.

New features and Changes

Sam 1.6 support:

  • Bam output now is designated version 1.6. (#1211)
  • Update the list of tags in SAMTag to include all reserved tags:
  • Deprecating tags that are deprecated in the sam spec, and deprecating SAMTagUtil, it's methods have been merged into SAMTag (#1208, #1227)
  • Added first class Description field to SAMSequenceRecord (#1209)
  • Deprecate SQTagUtil (#1214)

Known issue:

  • non-ascii unicode characters are not supported even though these are now allowed in certain fields. (#1202)

Addition of method to FeatureCodec

  • new method FeatureCodec.getPathToDataFile(String path)
    This allows a new class of codecs that identify a different file as readable from the one that actually contains the data. This has a default implementation and should require no changes from downstream users unless they have custom implementations of FeatureReader that do not go through AbstractFeatureReader (#1223)

More CRAM work:

Work on refactoring and improving the cram code continues.

  • Add hashCode() to classes with equals() and clean up equals() (#1222)
  • DataSeries/DataReader/DataWriter refactor (#1219, #453)
  • Be explicit about spec IDs instead of using ordinal() (#1221)
  • More encoding tests + updates (#1203)

Other Updates

Removing cruft leftover from JAXB (#1207)
Update the README with working test examples (#1225, #984)
Getter for generic fields in VCFSimpleHeaderLine (#1212)

Assets 2