Commits · 11b612fcdfa1fdd2a2614148b5b1772954e62e70 · ORG.Asm / ORG.Annotate · GitLab

20 Nov, 2018 1 commit
- Check the translation for stop codon and add a pseudogene qualifier if · 11b612fc
```
present.
```
  Eric Coissac committed Nov 20, 2018
  11b612fc Browse Directory
11 May, 2018 1 commit
- Redirect output of pushd and popd to /dev/null · e6ce2c73
  Eric Coissac committed May 11, 2018
  
  e6ce2c73 Browse Directory
25 Jan, 2018 1 commit
- Final small changes to patch the bug related to complex filenames · c59d7b5e
  Eric Coissac committed Jan 25, 2018
  
  c59d7b5e Browse Directory
24 Jan, 2018 5 commits
- Always a new attempt to solve the bug... · 0a5ece1e
  Eric Coissac committed Jan 24, 2018
  
  0a5ece1e Browse Directory
- Comment out phase 2 CDS searching · ca048f8c
  Eric Coissac committed Jan 24, 2018
  
  ca048f8c Browse Directory
- Add missing file... · f71b0396
  Eric Coissac committed Jan 24, 2018
  
  f71b0396 Browse Directory
- Patch a bug to launch exonerate on complexe filename · e8357a63
  Eric Coissac committed Jan 24, 2018
  
  e8357a63 Browse Directory
- Patch a bug to launch exonerate on complexe filename · fd381611
  Eric Coissac committed Jan 24, 2018
  
  fd381611 Browse Directory
23 Jan, 2018 1 commit
- Patch a bug blocking the exonerate execution when the genome filename is · a9da8eab
```
too long or complex
```
  Eric Coissac committed Jan 23, 2018
  a9da8eab Browse Directory
18 Jan, 2018 1 commit
- Patch a bug in the final sequence formating occuring when the input · 213735f5
```
sequence has not 60 char per line
```
  Eric Coissac committed Jan 18, 2018
  213735f5 Browse Directory
20 Oct, 2016 1 commit
- Allows for reporting · af7999b0
  Eric Coissac committed Oct 20, 2016
  
  af7999b0 Browse Directory
09 Oct, 2016 4 commits
- Patch the new ycf1 specific parameters · 66f848b3
  Eric Coissac committed Oct 09, 2016
  
  66f848b3 Browse Directory
- Add specific exonerate parameters for ycf1 · c956dde7
  Eric Coissac committed Oct 09, 2016
  
  c956dde7 Browse Directory
- For a given protein consider only cluster with at list a score of 95% of · cfdc6fcd
```
the best score
```
  Eric Coissac committed Oct 09, 2016
  cfdc6fcd Browse Directory
- Change awk to $AwkCmd · 79d7c6cc
```
Signed-off-by: Eric Coissac <eric.coissac@metabarcoding.org>
```
  Eric Coissac committed Oct 09, 2016
  79d7c6cc Browse Directory
06 Oct, 2016 5 commits
- Change some parameters in program calls · 3ed87608
  Eric Coissac committed Oct 06, 2016
  
  3ed87608 Browse Directory
- Change some blastx parametter to get better matches by taking into · 6600123f
```
account intron size and the good genetic code
```
  Eric Coissac committed Oct 06, 2016
  6600123f Browse Directory
- Switch to the speedup mode because of the slow down imposed by the new · 30f2caea
```
exonarate parametters
```
  Eric Coissac committed Oct 06, 2016
  30f2caea Browse Directory
- Make changes to better detect pseudo genes frameshited and annotate them · d827908d
```
correctly
```
  Eric Coissac committed Oct 06, 2016
  d827908d Browse Directory
- Add the management of pseudogenes · 26d91366
  Eric Coissac committed Oct 06, 2016
  
  26d91366 Browse Directory
05 Oct, 2016 1 commit
- A new set of protein cleaned for the CDS detector prepared using the · e30a53b5
```
clusterizecore.sh script from the detectors/cds/lib folder.

The CDS detector is now modified to use the clean.fst files.
```
  Eric Coissac committed Oct 05, 2016
  e30a53b5 Browse Directory
25 Apr, 2016 1 commit
- First trial to automatcally cleanup the core CDS database · dc61a618
  Eric Coissac committed Apr 25, 2016
  
  dc61a618 Browse Directory
13 Apr, 2016 3 commits
- call explicitely tcsh to workaround a path bug · e6c05a69
  Eric Coissac committed Apr 13, 2016
  
  e6c05a69 Browse Directory
- Change tha dash bang of the csh shell scripts · 115a1955
  Eric Coissac committed Apr 13, 2016
  
  115a1955 Browse Directory
- Add the latest tcsh able to deal with large PATH (at least 4096) · 32011d9b
  Eric Coissac committed Apr 13, 2016
  
  32011d9b Browse Directory
18 Dec, 2015 1 commit
- Add the name of the org.annot pipeline in the CDS inference · 497194fa
  Eric Coissac committed Dec 18, 2015
  
  497194fa Browse Directory
15 Nov, 2015 1 commit
- minor addition in cds/compare · e865ea93
  Alain Viari committed Nov 15, 2015
  
  e865ea93 Browse Directory
14 Nov, 2015 2 commits
- removed need of R igraph from chlorodb/subdb · 574aace9
  Alain Viari committed Nov 14, 2015
  
  574aace9 Browse Directory
- minor bug in chlorodb · 7017655a
  Alain Viari committed Nov 14, 2015
  
  7017655a Browse Directory
13 Nov, 2015 5 commits
- cds test on core and shell · 9be1f2c2
  Alain Viari committed Nov 13, 2015
  
  9be1f2c2 Browse Directory
- cds go_test bug fixed · f73133dc
  Alain Viari committed Nov 13, 2015
  
  f73133dc Browse Directory
- added test for chlorodb · 639cbbdc
  Alain Viari committed Nov 13, 2015
  
  639cbbdc Browse Directory
- add doc for chlorodb · 55fd2882
  Alain Viari committed Nov 13, 2015
  
  55fd2882 Browse Directory
- cds/tools/chlorodb added · 0579e878
  alain viari committed Nov 13, 2015
  
  0579e878 Browse Directory
11 Nov, 2015 1 commit
- summary added in comparison · 9a267727
  alain viari committed Nov 11, 2015
  
  9a267727 Browse Directory
10 Nov, 2015 2 commits
- fixed too many partial CDS bug · d733a46f
  alain viari committed Nov 10, 2015
  
  d733a46f Browse Directory
- added cds/tools compare and chrlorodb · 31633e6b
  alain viari committed Nov 10, 2015
  
  31633e6b Browse Directory
09 Nov, 2015 1 commit
- added cds/tools/compare · 07fb256b
  alain viari committed Nov 09, 2015
  
  07fb256b Browse Directory
08 Nov, 2015 2 commits
- go_pass1 moved to bin · 6be837df
  alain viari committed Nov 09, 2015
  
  6be837df Browse Directory
- fixed bug : CDS product not quoted · 412798e7
  alain viari committed Nov 08, 2015
  
  412798e7 Browse Directory