Commits · 325130bbedb3b0427ba39b93b6b3bc0b48f91bb4 · Mirrors / mutalyzer

Nov 24, 2011

Add strandedness to BED tracks · 325130bb

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@423 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

325130bb

Some code cleanup and fixes · 7d0c55cd

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@422 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

7d0c55cd

Merge r404-420 from trunk · 94251d65

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@421 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

94251d65

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

Merge r402 from trunk to browser-link-branch · 56335113

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@404 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

56335113

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 21, 2011

Fix url in BED track · df171de1

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@396 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

df171de1

Fix positions in BED track on reverse strand · 892ae9b7

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@395 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

892ae9b7

Oct 20, 2011

Implement BED tracks for Genome Browser · 8402dae3

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@394 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

8402dae3

Oct 12, 2011

Properly implement link to variant region in Genome Browser · 3b048179

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@393 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

3b048179

Merge r391 from trunk · 31527758

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@392 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

31527758

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

Fix Genome Browser link (issue #61) · 6b270da8

Vermaat authored 13 years ago

Link to UCSC Genome Browser now has a more proper implementation. Still todo
is error checking and such.

It uses the same infrastrucure as the position converter and is thus also
limited to variants on transcripts with c. notations.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@390 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

6b270da8

Merge r380-r388 from trunk to browser-link-branch · b58561a8

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@389 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

b58561a8

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

Quick hack as proof of concept implementation · 46b9c88b

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@379 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

46b9c88b

Create browser-link-branch from trunk · 692f4b15

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@378 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

692f4b15

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