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@@ -1,3 +1,66 @@
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-------------------------------------------------------------------
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Fri Mar 28 10:44:21 UTC 2025 - Stefan Brüns <stefan.bruens@rwth-aachen.de>
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- Update to version 1.21:
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* Extend annot-tsv with several new command line options.
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* Allow annot-tsv -a to rename annotations.
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* Extend annot-tsv --overlap to be able to specify the overlap
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fraction separately for source and target.
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* Added new APIs to facilitate low-level CRAM container
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manipulations, used by the new samtools cat region
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filtering code.
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* Some speed improvements.
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For a complete list of changes, see
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https://github.com/samtools/htslib/releases/tag/1.21
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-------------------------------------------------------------------
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Mon Jul 15 12:17:55 UTC 2024 - jun wang <jgwang@suse.com>
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- Update to version 1.20
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* When working on named files, bgzip now sets the modified and
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access times of the output files it makes to match those of
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the corresponding input
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* It's now possible to use a -o option to specify the output
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file name in bgzip
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* Improved error faidx error messages
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* Faster reading of SAM array (type "B") tags. These often turn
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up in ONT and PacBio data
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* Improved validity checking of base modification tags
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* mpileup overlap removal now works where one read has a
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deletion
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* The S3 plugin can now find buckets via S3 access point aliases
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* Added a --threads option (and -@ short option) to tabix
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* tabix can now index Graph Alignment Format (GAF) files
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* Security fix: Prevent possible heap overflow in
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cram_encode_aux() on bad RG:Z tags
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* Security fix: Prevent attempts to call a NULL pointer if
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certain URL schemes are used in CRAM @SQ UR: tags
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* Security fix: Fixed a bug where following certain AWS S3
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redirects could downgrade the connection from TLS
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(i.e. https://) to unencrypted http://. This could happen when
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using path-based URLs and AWS_DEFAULT_REGION was set to a
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region other that the one where the data was stored
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* Fixed arithmetic overflow when loading very long references
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for CRAM
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* Fixed faidx and CRAM reference look-ups on compressed fasta
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where the .fai index file was present, but the .gzi index of
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compressed offsets was not
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* Fixed BCF indexing on-the-fly bug which produced invalid
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indexes when using multiple compression threads
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* Ensure that pileup destructors are called by
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bam_plp_destroy(), to prevent memory leaks
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* Ensure on-the-fly index timestamps are always older than the
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data file. Previously the files could be closed out of order,
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leading to warnings being printed when using the index
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* To prevent data corruption when reading (strictly invalid)
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VCF files with duplicated FORMAT tags, all but the first copy
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of the data associated with the tag are now dropped with a
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warning
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* Fixed a bug introduced in release 1.19 (PR #1689) which broke
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variant record data if it tried to remove an over-long tag
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* Changed error to warning when complaining about use of the CG
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tag in SAM or CRAM files
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-------------------------------------------------------------------
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Wed Jan 3 01:40:50 UTC 2024 - Stefan Brüns <stefan.bruens@rwth-aachen.de>
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