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)
Commits
4a4024a Fix temporary directory hijacking or temporary directory information disclosu...
9fd0ecf Disable codecov until we can fix the uploader (#1622)
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Bumps htsjdk from 2.21.0 to 3.0.1.
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Sourced from htsjdk's releases.
... (truncated)
Commits
4a4024aFix temporary directory hijacking or temporary directory information disclosu...9fd0ecfDisable codecov until we can fix the uploader (#1622)347c0acFix EdgeReadIterator (#1616)d15a5baAdded ULTIMA and ELEMENT as valid value for RG-PL according to SAM spec. (#1619)489c419Support CRAM reference regions. (#1605)f461401Silence AsciiLineReader warning when creating a FASTA sequence index (#1559)1449decSupport loading of CSI from URLs/streams. #1507 (#1595)22aec67Fix decoding of CRAM Scores read feature during normalization. (#1592)70e4259Remove unnecessary println in test (#1602)6507249Make the CRAM MD5 failure message more user friendly. (#1607)Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting
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