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@lbergelson lbergelson released this 15 Nov 22:57
· 394 commits to master since this release
2.13.0
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lbergelson Louis Bergelson
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Learn about vigilant mode.
68189f3
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Learn about vigilant mode.

KNOWN ISSUES:

This version introduced a regression that can cause tools using sorting collections to crash. #1029
You may want to wait until 2.13.1 to upgrade.

This release includes assorted bug fixes and API improvements.

There is a new validation in SamFileValidation to check that records include quality scores. Records without quality scores are valid SAM records, but will often cause problems in downstream tools. This change means some files which previously validated will now emit warnings.

Deprecations:

The term not primary has been a longstanding cause of confusion in htsjdk. Deprecating methods that refer to notPrimary and replacing them with methods that refer to secondary. This should hopefully reduce confusion surrounding secondary and supplementary reads.

Removals:

the long deprecated SAMRecordUtil has been removed

Complete change list:

68189f3 Adds option to validator to skip mate validation (#1025)
060047e include cause when SAMFileWriterFactory rethrows exceptions (#1023)
0ab0667 More support for java.nio.Path: DiskBackedQueue and SortingCollection (#910)
889df1c Test that all the @DataProviders are successful (#1000)
5f90d4f Fix VCFFileReader.fromVCF throws an NPE when input contains no CONTIG lines #978 (#988)
82f9044 new SAM validation warning for missing quality scores (#993)
2a494dd Fix BufferedLineReader peek() at end of line with Windows line endings. (#1002)
4664c62 Add SamReaderFactory.referenceSequence(java.nio.Path) (#1006)
1efe018 Remove deprecated SAMRecordUtil (#950)
e45e448 Ability to opt-out of logging all failed intervals for LiftOver (#995)
e730d03 Add support for GZI index (#997)
d8e037a fixing resource leak in VCFFileReader (#1013)
d3e85e0 VariantContextFilter extends Predicate (#1010)
5df68ce Some refactoring of the Strand enum adding decoding (string and char) functionality. (#986)
3ac309c Add out/ to .gitignore (#1009)
d045c63 Deprecate 'not-primary' in favor of secondary along HTSJDK (#977)
bd4eac3 defining <NON_REF> allele in htsjdk, where it belongs. (#1007)
26eada2 Fixed ENA url to use https (instead of http) (#1004)
c9cab31 Remove redundant use of DataOutputStream when passing to BinaryCodec. (#1001)

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