Commits · 79d7c6cc4333c8f72cef71f9c5323c151bb0e6b7 · ORG.Asm / ORG.Annotate

09 Oct, 2016 1 commit
- Change awk to $AwkCmd · 79d7c6cc
  Eric Coissac authored Oct 09, 2016
```
Signed-off-by: Eric Coissac <eric.coissac@metabarcoding.org>
```
  79d7c6cc
06 Oct, 2016 5 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
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exonarate parametters
```
  30f2caea
- Make changes to better detect pseudo genes frameshited and annotate them · d827908d
  Eric Coissac authored Oct 06, 2016
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correctly
```
  d827908d
- Add the management of pseudogenes · 26d91366
  Eric Coissac authored Oct 06, 2016
  
  26d91366
05 Oct, 2016 1 commit

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

02 May, 2016 2 commits
- Add a patch for chloroplast annotation when no inverted repeats are · 7e3ddd41
  Eric Coissac authored May 02, 2016
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detected
```
  7e3ddd41
- Add annotation of nuclear rDNA cistron · ee54019d
  Eric Coissac authored May 02, 2016
  
  ee54019d
25 Apr, 2016 1 commit
- First trial to automatcally cleanup the core CDS database · dc61a618
  Eric Coissac authored Apr 25, 2016
  
  dc61a618
13 Apr, 2016 3 commits
- call explicitely tcsh to workaround a path bug · e6c05a69
  Eric Coissac authored Apr 13, 2016
  
  e6c05a69
- Change tha dash bang of the csh shell scripts · 115a1955
  Eric Coissac authored Apr 13, 2016
  
  115a1955
- Add the latest tcsh able to deal with large PATH (at least 4096) · 32011d9b
  Eric Coissac authored Apr 13, 2016
  
  32011d9b
18 Dec, 2015 3 commits
- Add the name of the org.annot pipeline in the CDS inference · 497194fa
  Eric Coissac authored Dec 18, 2015
  
  497194fa
- Specify the genetic code during the aragorn call. · 6f18008c
  Eric Coissac authored Dec 18, 2015
  
  6f18008c
- Close #15. Actually the bug in intron location was related to a · dac4fb73
  Eric Coissac authored Dec 18, 2015
```
misinterpretation of the aragorn output format. Now tRNA, and intron
location are coherent with most of the locations extracted from genbank
file with one or 2 base pairs of difference.
```
  dac4fb73
28 Nov, 2015 1 commit
- Patch a bug on the generation of the location of tRNA for gene on · 72990545
  Eric Coissac authored Nov 28, 2015
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reverse complement strand with an intron.
```
  72990545
15 Nov, 2015 1 commit
- minor addition in cds/compare · e865ea93
  Alain Viari authored Nov 15, 2015
  
  e865ea93
14 Nov, 2015 2 commits
- removed need of R igraph from chlorodb/subdb · 574aace9
  Alain Viari authored Nov 14, 2015
  
  574aace9
- minor bug in chlorodb · 7017655a
  Alain Viari authored Nov 14, 2015
  
  7017655a
13 Nov, 2015 5 commits
- cds test on core and shell · 9be1f2c2
  Alain Viari authored Nov 13, 2015
  
  9be1f2c2
- cds go_test bug fixed · f73133dc
  Alain Viari authored Nov 13, 2015
  
  f73133dc
- added test for chlorodb · 639cbbdc
  Alain Viari authored Nov 13, 2015
  
  639cbbdc
- add doc for chlorodb · 55fd2882
  Alain Viari authored Nov 13, 2015
  
  55fd2882
- cds/tools/chlorodb added · 0579e878
  alain viari authored Nov 13, 2015
  
  0579e878
11 Nov, 2015 1 commit
- summary added in comparison · 9a267727
  alain viari authored Nov 11, 2015
  
  9a267727
10 Nov, 2015 2 commits
- fixed too many partial CDS bug · d733a46f
  alain viari authored Nov 10, 2015
  
  d733a46f
- added cds/tools compare and chrlorodb · 31633e6b
  alain viari authored Nov 10, 2015
  
  31633e6b
09 Nov, 2015 7 commits
- Change minimum length for considering a match from 1000 to 100. · 6bd827ca
  Eric Coissac authored Nov 09, 2015
  
  6bd827ca
- remove the debug code · 7a805dc6
  Eric Coissac authored Nov 09, 2015
  
  7a805dc6
- Patch bug in the inverted repeats annotation · 73e4e016
  Eric Coissac authored Nov 09, 2015
```
Realize the annotation on the normalized chromosome
```
  73e4e016
- small modifications for the luke cluster · 55a83611
  Eric Coissac authored Nov 09, 2015
  
  55a83611
- change the call to awk · fa0b02e7
  Eric Coissac authored Nov 09, 2015
  
  fa0b02e7
- Patches for the cluster luke · 54cfd925
  Eric Coissac authored Nov 09, 2015
  
  54cfd925
- added cds/tools/compare · 07fb256b
  alain viari authored Nov 09, 2015
  
  07fb256b
08 Nov, 2015 5 commits
- go_pass1 moved to bin · 6be837df
  alain viari authored Nov 08, 2015
  
  6be837df
- fixed bug : CDS product not quoted · 412798e7
  alain viari authored Nov 08, 2015
  
  412798e7
- Switch from awk to gawk · 70b104ab
  Eric Coissac authored Nov 08, 2015
  
  70b104ab
- default PASS1_SPEEDUP set to 0 · 38d036b8
  alain viari authored Nov 08, 2015
  
  38d036b8
- CDS detector added · a72f30f9
  alain viari authored Nov 08, 2015
  
  a72f30f9