Changelog
=========
This is a record of changes made between each Mutalyzer release.
Version 2.0.beta-31
-------------------
Release date to be decided.
Version 2.0.beta-30
-------------------
Released on February 18th 2014.
- Handle NCBI Entrez response validation errors (fixes, among other things,
`LOVD#29 <https://humgenprojects.lumc.nl/trac/LOVD3/ticket/29>`_).
- Loosen error severity when CDS cannot be translated.
- Mutalyzer development migrated from Subversion to Git for version control.
Version 2.0.beta-29
-------------------
Released on October 11th 2013.
- Add Jonathan Vis attribution and COMMIT logo to about page.
Version 2.0.beta-28
-------------------
Released on September 18th 2013.
- Enable the HTTP/RPC+JSON web service to be used with POST requests.
Version 2.0.beta-27
-------------------
Released on June 18th 2013.
- Fix caching transcript-protein links from NCBI, reducing impact of NCBI
communication problems.
Version 2.0.beta-26
-------------------
Released on April 9th 2013.
- Added mm10 (Mouse) transcript mappings to position converter.
- LRG parser updated to LRG 1.7 schema (`#127
<https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/127>`_).
Version 2.0.beta-25
-------------------
Released on March 25th 2013.
- Detect incorrect exon annotation in transcript references.
- Move documentation to Trac.
- Exon table is included in `runMutalyzer` webservice results.
- Temporarily disable frameshift detection in experimental description
extractor (`#124
<https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/124>`_).
- Allow selectors on transcript references in position converter.
- Syntax checker now supports protein level variant descriptions.
Version 2.0.beta-24
-------------------
Released on December 10th 2012.
- Rename some warning codes (webservice API) (`#98
<https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/98>`_).
- Variants on mtDNA in position converter.
Version 2.0.beta-23
-------------------
Released on November 8th 2012.
No user-visible changes.
Version 2.0.beta-22
-------------------
Released on November 2nd 2012.
- Submitting batch jobs via the web services (`#115
<https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/115>`_).
- Allow for leading whitespace in batch job input (`#107
<https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/107>`_).
- New `descriptionExtract` webservice function.
- Name checker now includes description extractor output as an experimental
service.
- Slice chromosome by gene name in reference file loader is now case
insensitive (`#118
<https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/118>`_).
- Warn on missing positioning scheme (`#114
<https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/114>`_).
Version 2.0.beta-21
-------------------
Released on July 23rd 2012.
- Support compound variants in position converter.
- Support non-coding transcripts in position converter (`#102
<https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/102>`_).
- Move to new RPC library version, causing slight change in HTTP/RPC+JSON
webservice output (more wrappers around output), but fixes #104.
- Fix position converter for delins with explicit deleted sequence.
- Fix description update from Version 2.0.beta-20 to use- notation instead of
counting.
Version 2.0.beta-20
-------------------
Released on July 21st 2012.
- Disabled the ``-u`` and ``+d`` convention in favour of the official HGVS
recommendations.
Version 2.0.beta-19
-------------------
Released on June 21st 2012.
- Fix crash on inversions (`#99
<https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/99>`_).
Version 2.0.beta-18
-------------------
Released on June 7th 2012.
- Moved from soaplib to rpclib for webservices (`#66
<https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/66>`_).
- Added HTTP/RPC+JSON webservice (`#18
<https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/18>`_).
- Fixed name checker errors in some adjacent variants (`#83
<https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/83>`_).
- Name checker form now uses GET requests to support easier linking to result
pages.
- You can now specify chromosomes by name in the reference file loader (`#92
<https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/92>`_).
- Made batch daemon not crash on MySQL restarts (`#91
<https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/91>`_).
- Position converter now detects incorrect order in position ranges (`#95
<https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/95>`_).
- Added NBIC logo to 'about' page.
Version 2.0.beta-17
-------------------
Released on April 2nd 2012.
- Fixed crossmapping bug for some transcripts.
- Fixes for NCBI Entrez EFetch Version 2.0 release.
- Better chromosomal variant descriptions.
- Various smaller features and bugfixes.
Version 2.0.beta-16
-------------------
Released on March 1st 2012.
- Fixed position converter mapping info for some transcripts.
- Fixed deletion with deleted sequence length as argument.
Version 2.0.beta-15
-------------------
Released on February 20th 2012.
- Added 'Description Extractor' (see the main menu).
- Fixes for NCBI Entrez EFetch Version 2.0 release.
- Added chromosomal positions to `getTranscriptsAndInfo` webservice.
- Fixed chromosome slicing on reverse complement
- Fixed describing NOP variants with ``=``.
- Added Reference sequence info in `runMutalyzer` SOAP function response.
- Fixed mapping info for genes mapped to more than one chromosome.
- Various smaller features and bugfixes.
Version 2.0.beta-14
-------------------
Released on January 26th 2012.
- Added a SOAP service `getTranscriptsMapping`.
- Various smaller features and bugfixes.
Version 2.0.beta-13
-------------------
Released on January 25th 2012.
- Accept EX positioning scheme.
- Fix handling of LRG reference sequences.
- Various smaller features and bugfixes.
Version 2.0.beta-12
-------------------
Released on November 25th 2011.
- Accept plasmid reference sequences.
- View variant position in UCSC Genome Browser (only for transcript
references).
- Retry querying dbSNP if it does not respond the first time.
- Support reference GenBank files built from contigs.
- Add optional argument to SOAP service `numberConversion` to map chromosomal
locations to any gene.
- Various smaller features and bugfixes.
Version 2.0.beta-11
-------------------
Released on September 30st 2011.
- Major code refactoring:
- Mutalyzer is now structured as a proper Python package.
- Reworked installation and upgrade procedure.
- Remote installation using Fabric.
- Batch scheduler is now a proper system daemon.
- Use mod_wsgi (with web.py) instead of the deprecated mod_python.
- Added a lot of internal documentation.
- Introduce unit tests.
- Handle deletions of entire exons.
- Added a SOAP service `info`.
- Handle unknown (fuzzy) intronic positions.
- Automatic synchronization of database and cache between Mutalyzer
installations.
- Use NCBI instead of UCSC for transcript mapping info.
- Added a SOAP service `getdbSNPDescriptions`.
- Moved Trac and Subversion repository to new server.
- Implement HTTP HEAD method for ``/Reference/*`` locations.
- Added a SOAP service `ping`.
- Added an optional versions parameter to the SOAP service `getTranscripts`.
- Various smaller features and bugfixes.
Version 2.0.beta-10
-------------------
Released on July 21st 2011.
- Greatly reduce runtime for large batch jobs.
Version 2.0.beta-9
------------------
Released on June 27th 2011.
- Reworked the calculation of new splice site positions.
- Optionally restrict SOAP service `getTranscriptsAndInfo` transcripts to a
gene.
- Add raw variants to SOAP service `runMutalyzer` results.
- Provide webservice client examples.
- Various smaller features and bugfixes.
Older versions
--------------
The first lines of code for Mutalyzer 2.0 where written July 28th 2009, and
version 2.0.beta-8 was released on January 31st 2011. As far as Mutalyzer 1 is
concerned, archaeology is not really our field of research.