Commits · 66f848b351a6b8186ff03a7059aa167f39ed29a1 · ORG.Asm / ORG.Annotate

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 3 commits
- Add a patch for chloroplast annotation when no inverted repeats are · 7e3ddd41
  Eric Coissac authored May 02, 2016
```
detected
```
  7e3ddd41
- remove the printing of an extra empty line at the beginning of the embl · bba6581b
  Eric Coissac authored May 02, 2016
```
file
```
  bba6581b
- Add annotation of nuclear rDNA cistron · ee54019d
  Eric Coissac authored May 02, 2016
  
  ee54019d
28 Apr, 2016 1 commit
- Add ITSx to th src · 7f75da85
  Eric Coissac authored Apr 28, 2016
  
  7f75da85
25 Apr, 2016 3 commits
- Merge branch 'master' of ssh://git@git.metabarcoding.org/org-asm/org-annotate.git · 481c726b
  Eric Coissac authored Apr 25, 2016
  
  481c726b
- First trial to automatcally cleanup the core CDS database · dc61a618
  Eric Coissac authored Apr 25, 2016
  
  dc61a618
- Add a fasta1line function reformating the sequence with a line for the · 619dc4f5
  Eric Coissac authored Apr 25, 2016
```
header and a single line for the sequence
```
  619dc4f5
23 Apr, 2016 1 commit
- Add license · 08aa22fc
  Eric Coissac authored Apr 23, 2016
  
  08aa22fc
13 Apr, 2016 5 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
- Try to solve to "Warning: ridiculously long PATH truncated" message · 87663c6f
  Eric Coissac authored Apr 13, 2016
```
generated by the csh shell.

Perhaps will we have to avoid this shell ;-)
```
  87663c6f
- Solve #18 · 0ac744e9
  Eric Coissac authored Apr 13, 2016
  
  0ac744e9
04 Feb, 2016 1 commit
- Patch a bug leading to add extra quote to command line parametters · f84fd562
  Eric Coissac authored Feb 04, 2016
  
  f84fd562
27 Jan, 2016 1 commit
- Add the cd-hit program to the binaries · 0ecdb8d9
  Eric Coissac authored Jan 27, 2016
  
  0ecdb8d9
05 Jan, 2016 1 commit
- Patch a compilation bug for getopt · 0ea287f1
  Eric Coissac authored Jan 05, 2016
  
  0ea287f1
18 Dec, 2015 5 commits
- integrate options in the main script · e046ef88
  Eric Coissac authored Dec 18, 2015
  
  e046ef88
- Add the standard getopt external command allowing to deal with short and · 128f0656
  Eric Coissac authored Dec 18, 2015
```
long options in scripts
```
  128f0656
- 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
29 Nov, 2015 1 commit
- Ignore the build directory · 476e4070
  Eric Coissac authored Nov 29, 2015
  
  476e4070
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
```
reverse complement strand with an intron.
```
  72990545