Commits · 7e9fcd4ed6487e52562b274d87345e0e46f1458d · ORG.Asm / ORG.Annotate

05 Apr, 2018 7 commits
- Changes in .gitignore · 7e9fcd4e
  Eric Coissac authored Apr 05, 2018
  
  7e9fcd4e
- Switch to clustal-omega version 1.2.4 · f2eba5fb
  Eric Coissac authored Apr 05, 2018
  
  f2eba5fb
- Switch to version 1.2.38 of aragorn · 8fdde2e7
  Eric Coissac authored Apr 05, 2018
  
  8fdde2e7
- Change the notation algorithm to take advantage of the new CAU tRNA · 32650f41
  Eric Coissac authored Apr 05, 2018
```
reference library
```
  32650f41
- Modify script to accept compressed genome files · f816e3ce
  Eric Coissac authored Apr 05, 2018
  
  f816e3ce
- New version of the CAU tRNA reference database · 15ec72ca
  Eric Coissac authored Apr 05, 2018
  
  15ec72ca
- Simplify CAU tRNA reference database building to keep onlyCAU tRNA · 67dc4456
  Eric Coissac authored Apr 05, 2018
```
from plastomes where the three categories of CAU tRNA (Met/Ile/fMet)
are annotated
```
  67dc4456
30 Mar, 2018 2 commits
- Switch to clustalo version 1.2.4 · 0e15ea20
  Eric Coissac authored Mar 30, 2018
  
  0e15ea20
- Switch Aragorn to version 1.2.38 · 46bb3669
  Eric Coissac authored Mar 30, 2018
  
  46bb3669
25 Jan, 2018 1 commit
- Final small changes to patch the bug related to complex filenames · c59d7b5e
  Eric Coissac authored Jan 25, 2018
  
  c59d7b5e
24 Jan, 2018 7 commits
- Always a new attempt to solve the bug... · 0a5ece1e
  Eric Coissac authored Jan 24, 2018
  
  0a5ece1e
- Comment out phase 2 CDS searching · ca048f8c
  Eric Coissac authored Jan 24, 2018
  
  ca048f8c
- Add missing file... · f71b0396
  Eric Coissac authored Jan 24, 2018
  
  f71b0396
- Merge branch 'master' of · aeae3d48
  Eric Coissac authored Jan 24, 2018
```
ssh://git@git.metabarcoding.org/org-asm/org-annotate.git

Conflicts:
	detectors/cds/bin/do_exonerate.csh
```
  aeae3d48
- Patch a bug to launch exonerate on complexe filename · e8357a63
  Eric Coissac authored Jan 24, 2018
  
  e8357a63
- Patch a bug to launch exonerate on complexe filename · fd381611
  Eric Coissac authored Jan 24, 2018
  
  fd381611
- Patch a bug on numering the last nucleotide in the embl file · 626566f2
  Eric Coissac authored Jan 24, 2018
  
  626566f2
23 Jan, 2018 1 commit
- Patch a bug blocking the exonerate execution when the genome filename is · a9da8eab
  Eric Coissac authored Jan 23, 2018
```
too long or complex
```
  a9da8eab
18 Jan, 2018 2 commits
- Add logs to print the sequence length and if the sequence is reverse · ba55f354
  Eric Coissac authored Jan 18, 2018
```
complemented
```
  ba55f354
- Patch a bug in the final sequence formating occuring when the input · 213735f5
  Eric Coissac authored Jan 18, 2018
```
sequence has not 60 char per line
```
  213735f5
20 Oct, 2016 1 commit
- Allows for reporting · af7999b0
  Eric Coissac authored Oct 20, 2016
  
  af7999b0
12 Oct, 2016 1 commit
- Patch a serious bug in the embl formating of the sequence leading to · 92d73a91
  Eric Coissac authored Oct 12, 2016
```
frameshifts in the embl formated sequences
```
  92d73a91
09 Oct, 2016 7 commits
- Patch the new ycf1 specific parameters · 66f848b3
  Eric Coissac authored Oct 09, 2016
  
  66f848b3
- Force source to be the first feature · b78cd77b
  Eric Coissac authored Oct 09, 2016
  
  b78cd77b
- Add specific exonerate parameters for ycf1 · c956dde7
  Eric Coissac authored Oct 09, 2016
  
  c956dde7
- For a given protein consider only cluster with at list a score of 95% of · cfdc6fcd
  Eric Coissac authored Oct 09, 2016
```
the best score
```
  cfdc6fcd
- Change awk to $AwkCmd · 79d7c6cc
  Eric Coissac authored Oct 09, 2016
```
Signed-off-by: Eric Coissac <eric.coissac@metabarcoding.org>
```
  79d7c6cc
- Add ignore file · 3d1c76d9
  Eric Coissac authored Oct 09, 2016
  
  3d1c76d9
- Change the awk call by $AwkCmd · c5642bbb
  Eric Coissac authored Oct 09, 2016
  
  c5642bbb
06 Oct, 2016 6 commits
- Change some parameters in program calls · 3ed87608
  Eric Coissac authored Oct 06, 2016
  
  3ed87608
- Change some blastx parametter to get better matches by taking into · 6600123f
  Eric Coissac authored Oct 06, 2016
```
account intron size and the good genetic code
```
  6600123f
- Switch to the speedup mode because of the slow down imposed by the new · 30f2caea
  Eric Coissac authored Oct 06, 2016
```
exonarate parametters
```
  30f2caea
- Merge branch 'master' of ssh://git@git.metabarcoding.org/org-asm/org-annotate.git · 04e163d5
  Eric Coissac authored Oct 06, 2016
  
  04e163d5
- Make changes to better detect pseudo genes frameshited and annotate them · d827908d
  Eric Coissac authored Oct 06, 2016
```
correctly
```
  d827908d
- Add the management of pseudogenes · 26d91366
  Eric Coissac authored Oct 06, 2016
  
  26d91366
05 Oct, 2016 3 commits
- Merge branch 'master' of git.metabarcoding.org:org-asm/org-annotate · 284096bf
  Eric Coissac authored Oct 05, 2016
```
Conflicts:
	org-annotate.sh
```
  284096bf
- Add management of partial sequences · abd6112a
  Eric Coissac authored Oct 05, 2016
  
  abd6112a
- A new set of protein cleaned for the CDS detector prepared using the · e30a53b5
  Eric Coissac authored Oct 05, 2016
```
clusterizecore.sh script from the detectors/cds/lib folder.

The CDS detector is now modified to use the clean.fst files.
```
  e30a53b5
08 Aug, 2016 1 commit
- Add the possibility to annotate partially sequenced genome. · b4415ad2
  Eric Coissac authored Aug 08, 2016
```
Add the print of a source feature.
```
  b4415ad2
02 May, 2016 1 commit
- Add a patch for chloroplast annotation when no inverted repeats are · 7e3ddd41
  Eric Coissac authored May 02, 2016
```
detected
```
  7e3ddd41