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)
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 @dependabot rebase.
Dependabot commands and options
You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it
- `@dependabot merge` will merge this PR after your CI passes on it
- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it
- `@dependabot cancel merge` will cancel a previously requested merge and block automerging
- `@dependabot reopen` will reopen this PR if it is closed
- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
- `@dependabot use these labels` will set the current labels as the default for future PRs for this repo and language
- `@dependabot use these reviewers` will set the current reviewers as the default for future PRs for this repo and language
- `@dependabot use these assignees` will set the current assignees as the default for future PRs for this repo and language
- `@dependabot use this milestone` will set the current milestone as the default for future PRs for this repo and language
You can disable automated security fix PRs for this repo from the [Security Alerts page](https://github.com/allenday/gcp-popgen/network/alerts).
Bumps htsjdk from 2.20.3 to 3.0.1.
Release notes
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
@dependabot rebase.Dependabot commands and options
You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) - `@dependabot use these labels` will set the current labels as the default for future PRs for this repo and language - `@dependabot use these reviewers` will set the current reviewers as the default for future PRs for this repo and language - `@dependabot use these assignees` will set the current assignees as the default for future PRs for this repo and language - `@dependabot use this milestone` will set the current milestone as the default for future PRs for this repo and language You can disable automated security fix PRs for this repo from the [Security Alerts page](https://github.com/allenday/gcp-popgen/network/alerts).