Commits · 3fbd64c521cb42896e70d7eed4f95a716a2e954a · Mirrors / mutalyzer

Mar 26, 2013

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

Merge /branches/lrg-schema-update:r653-679 · a5afeb94

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@680 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

a5afeb94

Update LRG parser for new format · 3e0f15b5

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/lrg-schema-update@679 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

3e0f15b5

Merge /trunk:r653-677 · 68c42247

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/lrg-schema-update@678 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

68c42247

Complete previous commit · c427e6ec

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@677 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

c427e6ec

Transcript version update in unit tests · c519105f

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@676 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

c519105f

Open development for 2.0.beta-26 · 24024e0e

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@675 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

24024e0e

Release 2.0.beta-25 · 1c240962

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@673 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

1c240962

Mar 05, 2013

Note that slicing by gene uses current assembly · 69a30937

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@672 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

69a30937

Feb 25, 2013

Warning on non-adjacent exons in transcript reference · bd3ce1d1

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@671 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

bd3ce1d1

Feb 19, 2013

Move documentation to Trac · e752fa3f

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@670 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

e752fa3f

Feb 13, 2013

Minor monitor update · 7ef7dc4a

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@669 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

7ef7dc4a

Feb 12, 2013

Include exon table for selected transcript in webservice · 8590f9b9

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@668 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

8590f9b9

Use WNOMRNA_OTHER when appropriate (fixes #132) · c2b54871

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@667 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

c2b54871

Jan 22, 2013

Temporarily disable frameshift detection (#124) · 9a993899

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@666 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

9a993899

Jan 14, 2013

All hg19 mappings are noted as comments · ea2fb9db

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@665 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

ea2fb9db

Allow selectors on transcript references in position converter · 48a0b151
Vermaat authored 12 years ago
```
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@664 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
```
48a0b151

Accept trailing tabs in batch input · 2195ace0

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@663 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

2195ace0

SOAP example client for getGeneName · 9e872112

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@662 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

9e872112

Jan 07, 2013

Install script fixes · a84b70ea

Vermaat authored 12 years ago

- Syntax error in install script.
- Add missing 'organelle' value for a database record.
- Debian Wheezy python-mysql does not have the auto reconnect option, so
  disable it by default.
- MySQL 'grant' statements need host defined.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@661 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

a84b70ea

Jan 03, 2013

New version of the Mutalyzer 2.0 paper. · 0d858c63

Laros authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@660 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

0d858c63

Dec 20, 2012

Fix typo (thanks Gerard) · 17aa330d

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@659 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

17aa330d

NCBI mapping update command for build 37.5 · a439e9b1

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@658 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

a439e9b1

Fix bug in NCBI mapping update process · a61d9e83

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@657 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

a61d9e83

Dec 15, 2012

Fixed a highlighting bug in the text output. · 935340b1

Laros authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@656 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

935340b1

Added fancy printing of a protein to the console (handy for debugging). · 25b33ebe
Laros authored 12 years ago
```
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@655 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
```
25b33ebe

Dec 11, 2012

Update LRG parser for updated schema (incomplete) · e84bdeb8

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/lrg-schema-update@654 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

e84bdeb8

Create lrg-schema-update branch from trunk · 864aaa0f

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/lrg-schema-update@653 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

864aaa0f

Only show experimental services if we have the info · 74f517c2

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@652 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

74f517c2

Merge protein-branch r397-r650 in trunk · 219bf6ea

Vermaat authored 12 years ago

This consists of an updated HGVS parser accepting protein level descriptions
and some checks in the name checker to disable them for now.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@651 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

219bf6ea

Merge trunk r554-r649 in protein-branch · aab3de31

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/protein-branch@650 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

aab3de31

Open development for 2.0.beta-25 · bcb2b65d

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@649 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

bcb2b65d

Release 2.0.beta-24 · e80fd858

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@647 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

e80fd858

Dec 06, 2012

Added a Makefile for compiling papers. · d2ddaa08

Laros authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@646 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

d2ddaa08

Updated the Mutalyzer 2.0 paper. · 30ba85ef

Laros authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@645 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

30ba85ef

Nov 29, 2012

Rename some warning codes · 823f5bc0

Vermaat authored 12 years ago

Changed codes:

    WCDSSELECTED    -> WCDS
    WCDS            -> WCDS_OTHER
    WSPLICESELECTED -> WSPLICE
    WSPLICE         -> WSPLICE_OTHER


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@644 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

823f5bc0

Nov 28, 2012

Fixed the command line interface, it is not very pretty yet, but it now is · be574870

Laros authored 12 years ago

fully functional again.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@643 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

be574870

Frameshift detection error (#124) fixed. · 4e9bd5f2

Laros authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@642 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

4e9bd5f2