CHANGES.rst

Changelog

This is a record of changes made between each Mutalyzer release.

Version 2.0.15

Release date to be decided.

Version 2.0.14

Released on November 9th 2015.

• E-mail address is now optional in batch job website interface (#119).
• Use Mailcheck in the batch jobs form (#107).
• Optional email for batch jobs from webservices (#104).
• Process batch jobs grouped by email address (#101).
• Use interval binning scheme on transcript mappings (#100).
• Back translator interface (#74).
• Transcript-protein links are now cached in Redis (#94).
• Added Ter as a valid amino acid in the HGVS grammar (#90).
• Refactoring of unit tests (#88, #89).

Version 2.0.13

Released on October 1st 2015.

• Fix query bug in update transcript-protein links (#85).

Version 2.0.12

Released on September 30th 2015.

• Fix off-by-one in slicing chromosome by gene name (#79).
• Document scheme used for all positions and ranges (#79).
• Show diff for variant protein from non-reference start codon (#78).
• Visualise protein change, also with alternative start (#72).
• Translate alternative start to M, also in variant (#72).
• Added Baker's yeast (SacCer_Apr2011/sacCer3) assembly (#73).

Version 2.0.11

Released on August 6th 2015.

• Fix bug in recognizing p.(=) (was reported as p.?) (#65).

Version 2.0.10

Released on July 21st 2015.

• Don't crash the position converter on transcript mappings containing no exons (#63).
• Use the notation for an uncertain stop codon, e.g., p.(Gln730Profs*?) instead of p.(Gln730Profs*96) when a variant results in a frame shift or extension and we don't see a new stop codon in the RNA (#57).
• Added Dog (Broad CanFam3.1/canFam3) assembly for position converter (#56).

Version 2.0.9

Released on July 9th 2015.

• Improvements in encoding detection of uploaded batch files (#52, #53).
• Usability improvements in reading DNA for description extractor (#54).

Version 2.0.8

Released on May 27th 2015.

• The HGVS variant description extractor package is available through the Description Extractor interface (#1).
• GitHub project moved from LUMC/mutalyzer to mutalyzer/mutalyzer.

Version 2.0.7

Released on March 27th 2015.

• Return fault code and description on RPC service errors (#31).
• Use esummary 2.0 response format (#32).

Version 2.0.6

Released on February 10th 2015.

• Added getGeneLocation webservice method. Given a gene symbol and optional genome build, it returns the location of the gene (#28).
• Discard incomplete genes in genbank reference files (#26).

Version 2.0.5

Released on December 16th 2014.

• New website layout by Landscape (GitLab!26).
• Source code moved from GitLab to GitHub.
• Automated unit tests on Travis CI (#16).
• Developer documentation hosted on Read the Docs (#17).

Version 2.0.4

Released on November 19th 2014.

• Many string encoding related fixes. Summarizing, Mutalyzer should now be completely aware of input and output string encodings, in all interfaces. Internally, all strings are unicode strings. This comes with minor changes in the webservice definitions, which most clients will probably not notice (GitLab!25).
• Don't crash on mail errors in the batch scheduler (GitLab#30).
• Fix importing transcript mappings from UCSC database (GitLab#9).
• Rename GRCh36 to NCBI36 (GitLab#8).
• Updated all Python dependencies to their latest versions.
• Mutalyzer is now Open Source! Source code is available under the AGPL and documentation under the CC-by-sa license.

Version 2.0.3

Released on September 20th 2014.

• Fix several error cases in LOVD2 view on the name checker.

Version 2.0.2

Released on October 9th 2014.

• Fix incorrect GRCm38 chromosome accession number versions.
• Fix crash in position converter batch jobs.
• Upgrade the webservice library we use (Spyne, from 2.10.10 to 2.11.0). This potentially affects behaviour of both our SOAP and HTTP/RPC+JSON webservices, although our tests did not show any problems.

Version 2.0.1

Released on September 27th 2014.