New module can be found here:

    https://github.com/mutalyzer/crossmapper

Release 2.0.21

Fix typo in batch SNP converter

Drop Reference.geninfo_identifier

Release 2.0.20

Continue execution in check_variant() after EINVALIDTRANSVAR

Accept transcript accession number as transcript variant identifier.

mkroon authored Jun 15, 2016 and Vermaat committed Jun 15, 2016

* Added failing test with accession number as transcript variant
  identifier.
* Internally the accession number is translated to the transcript
  name (i.e. v-number) and subsequent processing is untouched.

Legend output in runMutalyzer

mkroon authored Jun 13, 2016 and Vermaat committed Jun 15, 2016

* Introduced LegendRecord in spyne model.
* Copy legend of variantchecker's output to the result of the RPC handler.

Move dbSNP query to ncbi module

This removes 25% of the code from the Retriever module which didn't
really belong there in the first place.

No output object is used anymore, a simple exception is thrown on
connection errors. We also removed the auto retry around the Entrez call
which I think didn't fix a problem that's ours to fix and added a lot of
complexity.

Revert adding Reference.version column

While working on this, I came to the conclusion it's not a good idea to
split accession and version. It introduces a lot of complexity for
little benefit.

In general, Mutalyzer always sees 'accession.version' as the identifier
of the reference and because we always want exact identifiers, there is
little need for accession numbers without version.

The most obvious use case I see for a split is that we can easily query
available references with a certain accession, not taking version into
account, as a way to inform the user when a specific reference
identifier was not found. But I guess we better have this use case as
the exception, and make our life easier for the rest.

So I guess I'm aborting this for now. Addition of the `version` column
has already landed in the master branch, but this is easy to roll
back. The original column has not yet been touched in master.

Add Reference.version column

Keep Reference.geninfo_identifier

This corrects #396 in which we were a bit too quick actually dropping
the column. As per our migration policy, we should first update the code
to work without the column, then drop the column at least one release
later.

Remove support for GI numbers

The NCBI is phasing out the use of sequence GIs, so we have no other
choice than to drop support for them.

https://www.ncbi.nlm.nih.gov/news/03-02-2016-phase-out-of-GI-numbers/

Fixes #349

Drop Reference.slice_* and Reference.download_url

Follow-up to #387, fixes #389

Fix data migrations for Reference.source

Due to a bug in the data migrations for the new `Reference.source`
column introduced in #387 and #392, the start position for references
created as a slice was used as both start and stop position in the new
column for storing this data.

This commit fixes these migrations and on top of this adds a new
migration which corrects any values set by the old migrations (in case
they were run before this fix). The original columns for these values
have not yet been dropped, so no data has been lost.

Thanks @ifokkema for reporting this issue.

Fixes #393

Add NOT NULL constraint on Reference.source

Follow-up to #387, fixes #388

Release 2.0.19