Bump com.github.samtools:htsjdk from 2.13.1 to 3.0.1 in /dbsnp-importer

[dependabot]

Bumps com.github.samtools:htsjdk from 2.13.1 to 3.0.1.

Release notes

Sourced from com.github.samtools:htsjdk's releases.

3.0.1

Fix for a long standing vulnerability around temporary directory creation which could expose data to malicious users with access to a shared system. See for more information #1617

Compatibility note:

The previous implementation of IOUtil.createTempDir() could accept a prefix with a complete file path: IOUtil.createTempDir("path/to/my/tempdir/prefix", ""). The new implementation will now throw in that case. You can use Files.createTemporaryDirectory(path, prefix) for those use cases instead.

4a4024a97 Fix temporary directory hijacking or temporary directory information disclosure (#1621) 9fd0ecf21 Disable codecov until we can fix the uploader (#1622) 347c0ac57 Fix EdgeReadIterator (#1616) d15a5bacb Added ULTIMA and ELEMENT as valid value for RG-PL according to SAM spec. (#1619)

3.0.0

Htsjdk 3.0.0: Revenge of the Simple Allele

This is the first htsjdk with a major version increase in a long time. We bumped it to indicate there are some breaking changes that will potentially require downstream code changes. Notably, Allele became an interface instead of a concrete class. SimpleAllele may be used as a replacement if you have classes which previously subclassed allele.

New Plugin Infrastructure: 6a60de7c2 Move API marker annotations into new annotation package. (#1558) 7ac95d5f7 Plugin framework and interfaces for versioned file format codecs (#1525) d40fe5412 Beta implementation of Bundles. (#1546)

CRAM 489c4192d Support CRAM reference regions. (#1605) 22aec6782 Fix decoding of CRAM Scores read feature during normalization. (#1592) 6507249a4 Make the CRAM MD5 failure message more user friendly. (#1607) b5af659e6 Fix restoration of read base feature code. #1379 (#1590) e63c34a92 Ignore TC, TN on CRAM read (#1578)

BAM/SAM 1449dec45 Support loading of CSI from URLs/streams. #1507 (#1595) a38c78d6c Add an option to SAMFileWriter to disable checking of ordering of rec… (#1599) 51aa6ed2b Validate that SAM header tag keys are exactly 2 characters long (#1561) fbd9e96d5 Deprecate OTHER as a PL value (#1552) d5f7e106b Adding PL Tag 'DNBSEQ' as the Platform/Technology for BGI/MGI (#1547)

Misc Improvements f461401e3 Silence AsciiLineReader warning when creating a FASTA sequence index (#1559) 8f82871c1 Update explain samflags script to python3 (#1585) 4ba4c0678 Update to new version of the snappy library which will work with M1 macs (#1580) e92706452 add predicate to GFF3Codec to give a chance to filter out some unused attributes (#1575) c647764b0 Some long reads tests using PacBio data. (#1564) 57c3f03eb remove hardcoded .idx (#1568) a94a32512 Add file extension to missing index error message #1512 (#1567) 74b827b67 Improve error message in IntervalTree (#1545) 7719274fe Htsget POST request support (#1529)

VCF: aac46ee6d Added GVCF mode for VariantContext type determination (#1544) d72d73b01 Add context to exception when the vcf file is invalid #1565 (#1566)

... (truncated)

Changelog

Sourced from com.github.samtools:htsjdk's changelog.

3.0.1 (2022-09-23)

Security fix: Fixes a vulnerability around temporary directory creation that could expose data to malicious users on shared systems (#1621).

Compatibility note: IOUtil.createTempDir() no longer accepts a prefix containing a full file path. Use Files.createTemporaryDirectory(path, prefix) instead.

• Fix temporary directory hijacking / information disclosure (#1621)
• Fix EdgeReadIterator (#1616)
• Add ULTIMA and ELEMENT as valid values for RG-PL (#1619)

3.0.0 (2022-06-03)

First major version bump. Primary breaking change: Allele is now an interface; SimpleAllele is the concrete implementation.

Breaking changes:

• Allele converted from concrete class to interface (#1454); ByteArrayAllele renamed to SimpleAllele (#1576)
• API marker annotations moved to new annotation package (#1558)
• New plugin framework for versioned file format codecs (#1525)

New features:

• CRAM reference regions support (#1605)
• CSI index loading from URLs/streams (#1595)
• Htsget POST request support (#1529)
• GVCF mode for VariantContext type determination (#1544)
• Beta implementation of Bundles (#1546)
• Fluent chaining setters for SAMSequenceRecord (#1563)
• Option to disable write-order checking in SAMFileWriter (#1599)

Bug fixes:

• Fix CRAM read base feature restoration (#1590)
• Fix CRAM scores read feature decoding during normalization (#1592)
• Respect genotype filtering when calculating AC/AN/AF (#1554)

Other:

• Add DNBSEQ platform tag for BGI/MGI sequencers (#1547)
• Deprecate OTHER as a PL value (#1552)
• Update snappy library for Apple Silicon compatibility (#1580)
• Migrate CI from Travis to GitHub Actions (#1572)

Commits

• 4a4024a Fix temporary directory hijacking or temporary directory information disclosu...
• 9fd0ecf Disable codecov until we can fix the uploader (#1622)
• 347c0ac Fix EdgeReadIterator (#1616)
• d15a5ba Added ULTIMA and ELEMENT as valid value for RG-PL according to SAM spec. (#1619)
• 489c419 Support CRAM reference regions. (#1605)
• f461401 Silence AsciiLineReader warning when creating a FASTA sequence index (#1559)
• 1449dec Support loading of CSI from URLs/streams. #1507 (#1595)
• 22aec67 Fix decoding of CRAM Scores read feature during normalization. (#1592)
• 70e4259 Remove unnecessary println in test (#1602)
• 6507249 Make the CRAM MD5 failure message more user friendly. (#1607)
• Additional commits viewable in compare view

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