File ncbi-blast.changes of Package ncbi-blast+

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File ncbi-blast.changes of Package ncbi-blast+

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Sat Sep 24 20:43:40 UTC 2022 - Stefan Brüns <stefan.bruens@rwth-aachen.de>

- Update to version 2.13.0
  * New features
    - Blastn_vdb and tblastn_vdb included in the 2.13.0 release.
    - Makeblastdb now produces a (JSON) metadata file about the
      database.
  * Improvements
    - TBLASTN can now handle database sequences up to 2 billion
      bases (was 1 billion)
    - Makeblastdb default volume size is now 3 billion bases
     (was 1 billion)
    - Dustmasker has a new option to replace low complexity
      regions with N's (hard masking)
    - Makeblastdb will issue an error message and exit if it
      encounters a sequence longer than the maximum supported
      size (2,147,483,647 letters).
  * Bug fixes
    - Rare problem with mutex that caused BLAST to crash.
    - Memory leaks.
- Update to version 2.12.0
  * New features
    - Threading by query batch (for BLASTN, BLASTP, BLASTX, RPSBLAST,
      and RPSTBLASTN) may more efficiently BLAST large numbers of
      queries, especially if the database is small or the search is
      limited by taxid. Use "-mt_mode 1" to enable this option.
    - Makeblastdb requires less virtual memory for smaller databases.
    - Makeprofiledb creates multiple volumes for a CDD database,
      which allows RPSBLAST to handle a larger number of records.
      The number of SMP files included in a volume can be controlled
      with the new -new_smp_vol option.
    - update_blastdb.pl now supports the "-showall pretty" option
      for databases hosted at the NCBI.
    - update_blastdb.pl now reports the database timestamp in
      ISO8601 format.
  * Bug fixes
    - Fixed phiblast core dump when -subject option is used.
- Use Python 3, wxWidgets 3.2 for building

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Wed Aug  4 09:00:21 UTC 2021 - Atri Bhattacharya <badshah400@gmail.com>

- Add ncbi-blast-no-return-from-non-void.patch: Fix non-void
  functions not returning any value; fixes build for openSUSE >=
  1550.

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Sat May 29 15:32:00 UTC 2021 - Matthias Mailänder <mailaender@opensuse.org>

- Update to version 2.11.0

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Tue Dec 11 08:19:34 UTC 2018 - Pierre Bonamy <flyos@mailoo.org>

- Readded rpsblast and use update-alternatives to allow co-installation
  with ncbi-tools (blast+ has higher priority)

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Mon Sep 10 14:09:00 UTC 2018 - flyos@mailoo.org

- Remove rpsblast from install to avoid file conflicts with "ncbi-blast"
  package from "ncbi" spec file

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Thu Sep  6 08:06:18 UTC 2018 - flyos@mailoo.org

- Change the name of the package to nbci-blast+ to be avoid conflicts
with ncbi-blast packaged in "ncbi" and to be aligned with other systems
(e.g. Debian world)
- Update to version 2.7.1
	* BLAST+ 2.7.1: October 23, 2017
	- Improvements::
	    Provided an upper limit on the number of threads for BLAST+ 
	search applications.
	    Improved performance of taxonomic name lookups.
	    Fixed Mac installers so they are interoperable with other NCBI 
	applications.
	    Reduced the amount of locking in BLASTDB reading library (CSeqDB).
	- Bug fixes::
	    Fixed race condition when using gilist parameter.
	    Fixed culling_limit bug with HSPs from different strands
	    Fixed dustmasker bug with long region of Ns
	    Fixed bl2seq problem with HTML output
	
	* BLAST+ 2.6.0: January 09, 2017
	- New features::
	    Handle bare accessions on blastdb_aliastool.
	    Change defaults for output formats 6, 7, and 10 to incorporate 
	version in accessions.
	- Improvements::
	    Add support for NCBI_DONT_USE_LOCAL_CONFIG and 
	NCBI_DONT_USE_NCBIRC environment variables.
	    Better runtime performance in blastdbcmd when the entry_batch 
	parameter is used.
	    SAM output improvements.
	    Changed gapped alignment starting point to minimize the chance to 
	produce sub-optimal alignments.
	    For custom matrices absent from the util/tables source file, use 
	BLOSUM62 for reporting number of positives.
	    Added long_seqids flag to blastdbcmd to use long (legacy) NCBI 
	Seq-id format.
	- Bug fixes::
	    Fixed issue with missing alignments in blastx.
	    Fixed problem processing accession.version in makeblastdb.
	    Fixed blastdbcmd problem with local IDs.
	    Removed memory leak for multi-threaded runs.
	    Fixed blastdbcmd crash when listing all entries and a sequence has 
	no title.
	    
	* BLAST+ 2.5.0: September 12, 2016
	- New features::
	    Composition based statistics for rpstblastn.
	    Added output format for taxonomic organism report.
	    Support for bare accessions in FASTA and BLAST reports.
	- Improvements::
	    -remote option connects to NCBI via HTTPS. This adds a dependency 
	on GNUTLS (see https://www.ncbi.nlm.nih.gov/books/NBK279690/)
	    Pre-fetch sequences for formatting.
	- Bug fixes::
	    Fixed improper functioning of output format 6 tokens ssciname, 
	staxid, sscinames and staxids.
	    tblastn core-dumps in multi-threaded mode.
	    Ensure stable sorting of results in multi-threaded mode.
	    Fixed incorrect percent identity in tabular format for sequences 
	containing selenocysteine.
	
	* BLAST+ 2.4.0: June 02, 2016
	- New features:
	    Introduced multi-threaded traceback for blastp, blastx, tblastn 
	and tblastx.
	    Added new tabular format specifiers for taxonomic information 
	(staxid, ssciname, scomname, sblastname, skingdom) that correspond to 
	the first subject ID.
	- Improvements:
	    Speed up makeblastdb runtime performance with input consisting of 
	many ambiguities.
	    Better support for 'bare' IDs in taxid_map option to makeblastdb.
	    Score U (selenocysteine) as C (not X) in protein-protein and 
	translated searches.
	- Bug fixes:
	    Corrected E-value computation in finite-size correction.
	    Removed memory leak from rpsblast.
	    Made handling of ambiguities in subjects identical when using 
	FASTA and BLAST database inputs.
	    makeblastdb no longer replaces tabs in definition line by '#'.
	    Corrected problem with spaces in database names on windows.
	    Corrected handling of subject_loc.
	
	* BLAST+ 2.3.0: December 21, 2015
	- New features:
	    Added new PSIBLAST command line options to support saving PSSM 
	and checkpoint files for each iteration and calculate checkpoint and 
	PSSM for the last iteration.
	    Added unique subject sequence query coverage to tabular output.
	    Added support single file JSON and XML2 Blast output format.
	    Beta release of SAM output format.
	    Treat N subject sequences, entered with the -subject argument 
	(bl2seq mode), as one search set rather than N sets.
	- Improvements:
	    makeblastdb ignores and warns users about empty sequences in 
	input.
	    BLAST+ only accepts "obinary" windowmasker files for performance 
	reasons.
	- Bug fixes:
	    Best hits processing multi-threaded context.
	    Fixed memory leak when invoking composition based statistics with 
	an argument of 2.
	    Return non-zero exit code when failing to write output file.
	    Use relative paths in XInclude file for multi-file XML2 output 
	format.
	    Fixed memory leak in blastx.
	    Fixed inconsistent XML2 output to standard output vs. file.
	    Fixed psiblast incorrectly processing large input MSA.
	    Fixed bug when running BLAST+ on windows with multiple threads.
	
	* BLAST+ 2.2.31: May 18, 2015
	- New features:
	    Added support for BLAST-XML2 specification.
	    Added support for JSON Blast output format.
	- Improvements:
	    Improved adaptive batch size algorithm to better handle small 
	databases.
	    Preface error/warning message(s) with name of the application.
	    Allow multiple deflines even without GIs.
	    Download more concise database information for -remote searches.
	- Bug fixes:
	    Fixed problem with makeblastdb's -max_file_sz.
	    Reenabled support for word size 5 in tblastn.
	    Fixed memory initialization problems.
	    Use score for sorting search results if evalue less than 1.0e-180.

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Thu May 21 08:47:02 UTC 2015 - mailaender@opensuse.org

- update to version 2.2.30

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Sun Sep 14 18:17:26 UTC 2014 - mailaender@opensuse.org

- update to version 2.2.29

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Wed Sep  5 19:26:40 UTC 2012 - scorot@free.fr

- remove unneeded version check in build requirements. Package
  builds fine even on old product

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Mon Sep  3 05:36:33 UTC 2012 - scorot@free.fr

- add -fpemissive gcc flag in order to fix build with gcc 4.7

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Fri Aug 31 08:32:50 UTC 2012 - mailaender@opensuse.org

- Update to Version 2.2.26+

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Wed Mar 30 00:00:00 UTC 2011 - r.h.h.koot@umcutrecht.nl

- Added patch to build on openSuSE 11.3

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Mon Jul 21 00:00:00 UTC 2008 - camacho@ncbi.nlm.nih.gov

- See ChangeLog file

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