Commits · d094cf4d4a398f9e270c6eed43c13bd177a21204 · Mirrors / mutalyzer

Nov 23, 2011

Fix reverse complement of number parameter in position converter · d094cf4d
Vermaat authored 13 years ago
```
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@420 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
```
d094cf4d

Try being forgiving in dbSNP queries by retrying · ad0860e5

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@419 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

ad0860e5

Nov 14, 2011

Fix crash on variant without reference (thx Ivar) · 5fdc74c3

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@418 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

5fdc74c3

Nov 10, 2011

Add restriction site effects to batch output · 383b55f8

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@417 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

383b55f8

Fix bugs due to implicit config refactoring · 20cbda9e

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@416 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

20cbda9e

Nov 08, 2011

Merge implicit-config-branch to trunk · 1a6251c8

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@412 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

1a6251c8

Merge r407, r409, r410 from trunk to implicit-config-branch · 974e2a55

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/implicit-config-branch@411 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

974e2a55

Retrieve full sequence for contig reference files · cff8ea36

Vermaat authored 13 years ago

Fixes #74.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@410 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

cff8ea36

Nov 04, 2011

Fix typo · b75860cb

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@409 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

b75860cb

Use implicit configuration object creation · ae2ae0c8

Vermaat authored 13 years ago

The old way of using the configuration file was by instantiating a Config
object which read the file. This instance was passed to every function and
object that might need it.

The new way is by simply calling config.get('name') to get the configuration
value for 'name'. This lazily reads the configuration file and the contents
are cached for future calls.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/implicit-config-branch@408 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

ae2ae0c8

Remove some old TODO items · 5b5160f9

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@407 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

5b5160f9

Create implicit-config-branch from trunk · d1e45249

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/implicit-config-branch@406 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

d1e45249

Nov 01, 2011

Convert genomic positions to any transcript · ca585e08

Vermaat authored 13 years ago

Add optional gene argument to the numberConvertion webservice method. If
present, it will convert genomic variants to any transcript of the given
gene, no matter how far away they are located (but on the same chromosome
of course). Fixes #70.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@402 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

ca585e08

Oct 11, 2011

Make install/upgrade scripts a bit more robust · 4e06a57c

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@391 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

4e06a57c

Oct 10, 2011

Give an error on protein reference sequences · 18e228a6

Vermaat authored 13 years ago

Until protein reference sequences are supported, give an error with a message
instead of crashing. Fixes #62.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@388 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

18e228a6

Accept IVS locations in Variant_info LOVD interface · 302ba055

Vermaat authored 13 years ago

The fix is a hack, basically copying the same functionality from the
namechecker. I think this should eventually be merged somehow.

Fixes #63


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@387 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

302ba055

Update default Mutalyzer location in cache-sync cronjob · f4a60125

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@386 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

f4a60125

Oct 07, 2011

Copy user config from install as root (fixes #64) · cd447389

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@385 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

cd447389

Do apt-get update before installing in pre-install script · d0682e4b

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@384 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

d0682e4b

Oct 06, 2011

Update development notes · 0b6bf436

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@383 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

0b6bf436

Oct 05, 2011

Update documentation · e7995ea2

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@382 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

e7995ea2

Oct 04, 2011

Fix for migration 001 (set default values) · e12d3c81

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@381 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

e12d3c81

Sep 30, 2011

Small documentation update · daf079e9

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@380 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

daf079e9

Open development for 2.0.beta-12 · 13440c94

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@375 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

13440c94

Release 2.0.beta-11 · 1b7fb8f9

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@373 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

1b7fb8f9

Merge refactor-mutalyzer-branch back into trunk · f48bd705

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@372 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

f48bd705

Fix bug in command line interface · feb61bba

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@371 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

feb61bba

Sep 29, 2011

Rename GenBank Uploader to Reference File Loader · 234ff625

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@370 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

234ff625

Sep 27, 2011

Add HEAD method to /Reference download · f8d9bab7

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@369 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

f8d9bab7

Fix crash in VariantInfo (thanks Ivo) · 6f20208c

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@368 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

6f20208c

Sep 26, 2011

Implement mod_wsgi daemon mode and zero-downtime upgrades · 9d901c20

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@367 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

9d901c20

New location for Trac · a0d5a066

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@366 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

a0d5a066

Sep 20, 2011

Fix uploading non-genbank files · 3fbe50a1

Vermaat authored 13 years ago

- Issue a warning instead of an UD number when a user uploads something
  that is not a genbank file (fixes #59).
- Fix a Heisenbug in the batch job unit tests. Wait a little before
  downloading the batch job results.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@365 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

3fbe50a1

Fix looping over homedirs in post-install script · dc934b6a

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@364 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

dc934b6a

Sep 19, 2011

Fix active menu highlighting on HTTPS · 917ecda7

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@363 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

917ecda7

Fix for getCache webservice unit test · ed8d8c45

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@362 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

ed8d8c45

Use NCBI mapping data from older build · a9029121

Vermaat authored 13 years ago

We previously used the NCBI mapping data for the current build, but now a new
build was just released, the mapping data is missing (they are waiting for the
data and it should be up soon).

For now, we just use the mapping data for the archived previous build (it is
the build we were using until now anyway).

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@361 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

a9029121

Fix bug in migration script · 85430fb0

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@360 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

85430fb0

Sep 14, 2011

Merge r356 from trunk · 357e229a

Vermaat authored 13 years ago

Added a ping() function to the webservice.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@359 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

357e229a

Sep 13, 2011

Use test mail address in batch unit tests · 1caa029b

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@358 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

1caa029b