Commits · 7124b0b416a9f7ad1b0613b5b63c5c197b6f3596 · Mirrors / mutalyzer

Mar 27, 2014
- Open development for 2.0.beta-32 · 7124b0b4
  Vermaat authored 11 years ago
  
  7124b0b4
- Bump version to 2.0.beta-31 · ca217bc3
  Vermaat authored 11 years ago
  
  View commits for tag mutalyzer-2.0.beta-31 mutalyzer-2.0.beta-31
  
  ca217bc3
- Link to announcement on the wiki · 2efde263
  Vermaat authored 11 years ago
  
  2efde263
Mar 26, 2014

In LRG, ignore transcripts without a fixed id · 289423f8

Vermaat authored 11 years ago

Because we don't know how to name them anyway. We also ignore genes
without any transcripts.

289423f8

In LRG, only support one CDS per transcript (ignore all others) · a89fcf46

Vermaat authored 11 years ago

The LRG model allows for more than one CDS per transcript (and each CDS
can be coupled with more than one transcript). The Mutalyzer gene model
does not allow that.

Previously, multiple CDSs per transcript where treated incorrectly (I
think), so now we just ignore any CDS except the first per transcript.

Unfortunately, it is a bit more involved to give good warnings for this,
so that is not implemented.

a89fcf46

Feb 18, 2014
- Open development for 2.0.beta-31 · 5c1e01dc
  Vermaat authored 11 years ago
  
  5c1e01dc
- Bump version to 2.0.beta-30 · 627006eb
  Vermaat authored 11 years ago
  
  View commits for tag mutalyzer-2.0.beta-30 mutalyzer-2.0.beta-30
  
  627006eb
Feb 17, 2014
- Handle NCBI Entrez response validation errors · a00f8ad1
  Vermaat authored 11 years ago
  
  a00f8ad1
Jan 02, 2014
- Fix installation via Fabric with latest setuptools/distribute · 4eab2c24
  Vermaat authored 11 years ago
  
  4eab2c24
Dec 23, 2013
- Loosen error severity when CDS cannot be translated · c2d67551
  Laros authored 11 years ago and Vermaat committed 11 years ago
  
  c2d67551
Dec 04, 2013
- Fix Windows line endings in INSTALL.md · b102f007
  Vermaat authored 11 years ago
  
  b102f007
Nov 22, 2013
- Fixed a typo. · cad97e88
  Laros authored 11 years ago
  
  cad97e88
Nov 14, 2013
- Merge branch 'svn-git-migration' of /home/git/repositories/mutalyzer/mutalyzer · 5b0afe22
  Vermaat authored 11 years ago
  
  5b0afe22
Nov 13, 2013

Migrate from Subversion to Git · 8b3d9fc0

Vermaat authored 11 years ago

The actual conversion of the repository was done using svn2git [1].

[1] https://github.com/nirvdrum/svn2git

8b3d9fc0

Nov 07, 2013

Add clearer instruction to Position Converter · bef2db0c

Vermaat authored 11 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@753 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

bef2db0c

Nov 05, 2013

Added the new description extractor. · 54bfe6d9

Laros authored 11 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@752 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

54bfe6d9

Oct 11, 2013

Open development for 2.0.beta-30 · b3cb63c7

Vermaat authored 11 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@751 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

b3cb63c7

Release 2.0.beta-29 · c73853fd

Vermaat authored 11 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@749 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

c73853fd

Add Jonathan Vis attribution and COMMIT logo to about page · b9b8af0a

Vermaat authored 11 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@748 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

b9b8af0a

Sep 30, 2013

Fix HGVS syntax description in name/syntax checker forms · ec1680db

Vermaat authored 11 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@747 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

ec1680db

Sep 19, 2013

Add tests for JSON webservice using POST requests · b91d657b

Vermaat authored 11 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@746 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

b91d657b

Sep 18, 2013

Release 2.0.beta-28 · 515fd45d

Vermaat authored 11 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@744 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

515fd45d

Update unit tests to pass with latest NCBI data · 4ddd28ad

Vermaat authored 11 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@743 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

4ddd28ad

Require Python werkzeug to be installed · b75fd9ae

Vermaat authored 11 years ago

This enables using POST requests for the JSON webservice.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@742 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

b75fd9ae

Jul 04, 2013

Fix missing fields in example config · e1aeaa14

Vermaat authored 11 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@703 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

e1aeaa14

Jun 18, 2013

Open development for 2.0.beta-28 · 0bc53d34

Vermaat authored 11 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@701 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

0bc53d34

Release 2.0.beta-27 · 5d42d883

Vermaat authored 11 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@699 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

5d42d883

Jun 12, 2013

Limited cache lifetime for mrna-protein links · 5c5f8dea

Vermaat authored 11 years ago

Rework the caching of transcript<->protein accession number links. If no
link is reported by the NCBI, this is now also cached. For these type of
negative links and the normal links, separate cache lifetimes can be
defined.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@698 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

5c5f8dea

May 21, 2013

Paper: exon deletions and fuzzy offsets · 4762914d

Vermaat authored 11 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@697 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

4762914d

Apr 09, 2013

No weird instance attribute names starting with double underscore · 206c51d9
Vermaat authored 11 years ago
```
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@694 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
```
206c51d9

Switch order of migrations 011 and 012 · 6a2299a3

Vermaat authored 11 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@693 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

6a2299a3

Open development for 2.0.beta-27 · fe567b67

Vermaat authored 11 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@692 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

fe567b67

Release 2.0.beta-26 · 3076481a

Vermaat authored 11 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@690 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

3076481a

Add help link for each module in the web interface · 304a8ab5

Vermaat authored 11 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@689 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

304a8ab5

Apr 08, 2013

Proposal for student project: MoBiLe 2013 · 945a659b

Vermaat authored 11 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@688 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

945a659b

Mar 26, 2013

Keep service usage counts in database · 6000f9fa

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@687 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

6000f9fa

Merge /branches/mapping-mouse:r682-684 · ab633aed

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@685 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

ab633aed

Configure default mapping database · 3fbd64c5

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mapping-mouse@684 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

3fbd64c5

Mar 25, 2013

Add mm10 (Mouse) transcript mappings · d27bbd08

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mapping-mouse@683 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

d27bbd08

Create mapping-mouse branch from trunk · 4052e854

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mapping-mouse@682 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

4052e854