Commits · master · ORG.Asm / ORG.Annotate · GitLab

20 Nov, 2018 4 commits
- Patch a bug leading to a double pseudogene tagging · 35e27b66
  Eric Coissac committed Nov 20, 2018
  
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- If proteins are looked for without stop adds an extra option · 318327af
```
PASS1_LOOK_FOR_PSEUDO allowing for searching with stop in a second time
(Pseudogene search).

The PASS1_ALLOW_STOP is set back to 0 and the new PASS1_LOOK_FOR_PSEUDO
is set to 1
```
  Eric Coissac committed Nov 20, 2018
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- Check the translation for stop codon and add a pseudogene qualifier if · 11b612fc
```
present.
```
  Eric Coissac committed Nov 20, 2018
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- Merge branch 'master' of ssh://git@git.metabarcoding.org/org-asm/org-annotate.git · 0eee2e07
  Eric Coissac committed Nov 20, 2018
  
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11 May, 2018 5 commits
- Add .DS_Store to the .gitignore files · b92f4196
  Eric Coissac committed May 11, 2018
  
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- Add .DS_Store to the .gitignore files · a543c30e
  Eric Coissac committed May 11, 2018
  
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- Correct .gitignore files · 9d27bea3
  Eric Coissac committed May 11, 2018
  
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- Redirect output of pushd and popd to /dev/null · e6ce2c73
  Eric Coissac committed May 11, 2018
  
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- Switch to version 2.4.0 of exonerate · c3d1cd54
  Eric Coissac committed May 11, 2018
  
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05 Apr, 2018 9 commits
- Freshly regerenrated CAU tRNA reference library with the new tool script · b2808b9d
  Eric Coissac committed Apr 05, 2018
  
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- Add eclipse project files · 96afe525
  Eric Coissac committed Apr 05, 2018
  
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- Changes in .gitignore · 7e9fcd4e
  Eric Coissac committed Apr 05, 2018
  
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- Switch to clustal-omega version 1.2.4 · f2eba5fb
  Eric Coissac committed Apr 05, 2018
  
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- Switch to version 1.2.38 of aragorn · 8fdde2e7
  Eric Coissac committed Apr 05, 2018
  
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- Change the notation algorithm to take advantage of the new CAU tRNA · 32650f41
```
reference library
```
  Eric Coissac committed Apr 05, 2018
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- Modify script to accept compressed genome files · f816e3ce
  Eric Coissac committed Apr 05, 2018
  
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- New version of the CAU tRNA reference database · 15ec72ca
  Eric Coissac committed Apr 05, 2018
  
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- Simplify CAU tRNA reference database building to keep onlyCAU tRNA · 67dc4456
```
from plastomes where the three categories of CAU tRNA (Met/Ile/fMet)
are annotated
```
  Eric Coissac committed Apr 05, 2018
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30 Mar, 2018 2 commits
- Switch to clustalo version 1.2.4 · 0e15ea20
  Eric Coissac committed Mar 30, 2018
  
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- Switch Aragorn to version 1.2.38 · 46bb3669
  Eric Coissac committed Mar 30, 2018
  
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25 Jan, 2018 1 commit
- Final small changes to patch the bug related to complex filenames · c59d7b5e
  Eric Coissac committed Jan 25, 2018
  
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24 Jan, 2018 7 commits
- Always a new attempt to solve the bug... · 0a5ece1e
  Eric Coissac committed Jan 24, 2018
  
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- Comment out phase 2 CDS searching · ca048f8c
  Eric Coissac committed Jan 24, 2018
  
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- Add missing file... · f71b0396
  Eric Coissac committed Jan 24, 2018
  
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- Merge branch 'master' of · aeae3d48
```
ssh://git@git.metabarcoding.org/org-asm/org-annotate.git

Conflicts:
	detectors/cds/bin/do_exonerate.csh
```
  Eric Coissac committed Jan 24, 2018
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- Patch a bug to launch exonerate on complexe filename · e8357a63
  Eric Coissac committed Jan 24, 2018
  
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- Patch a bug to launch exonerate on complexe filename · fd381611
  Eric Coissac committed Jan 24, 2018
  
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- Patch a bug on numering the last nucleotide in the embl file · 626566f2
  Eric Coissac committed Jan 24, 2018
  
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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
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18 Jan, 2018 2 commits
- Add logs to print the sequence length and if the sequence is reverse · ba55f354
```
complemented
```
  Eric Coissac committed Jan 18, 2018
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- 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
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20 Oct, 2016 1 commit
- Allows for reporting · af7999b0
  Eric Coissac committed Oct 20, 2016
  
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12 Oct, 2016 1 commit
- Patch a serious bug in the embl formating of the sequence leading to · 92d73a91
```
frameshifts in the embl formated sequences
```
  Eric Coissac committed Oct 12, 2016
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09 Oct, 2016 7 commits
- Patch the new ycf1 specific parameters · 66f848b3
  Eric Coissac committed Oct 09, 2016
  
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- Force source to be the first feature · b78cd77b
  Eric Coissac committed Oct 09, 2016
  
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- Add specific exonerate parameters for ycf1 · c956dde7
  Eric Coissac committed Oct 09, 2016
  
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- 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
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- Change awk to $AwkCmd · 79d7c6cc
```
Signed-off-by: Eric Coissac <eric.coissac@metabarcoding.org>
```
  Eric Coissac committed Oct 09, 2016
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- Add ignore file · 3d1c76d9
  Eric Coissac committed Oct 09, 2016
  
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- Change the awk call by $AwkCmd · c5642bbb
  Eric Coissac committed Oct 09, 2016
  
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