Commits · 30b6f5a2d1f939a767caa210d9f78def48d7d72a · ORG.Asm / ORG.Asm · GitLab

05 Nov, 2016 6 commits
- Change the rule to determine is probe sequences are proteins · 30b6f5a2
  Eric Coissac committed Nov 05, 2016
  
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- Supress the intermediate progression logging if the log is done on a tty · 5ab4154d
  Eric Coissac committed Nov 05, 2016
  
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- Add the logger to the call to scaffold · be2c5ba6
  Eric Coissac committed Nov 05, 2016
  
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- Add a new assembler property to the compact assembly objects · 6c213599
  Eric Coissac committed Nov 05, 2016
  
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- Change unfold command according to the new unfold algorithm · 80be8f89
  Eric Coissac committed Nov 05, 2016
  
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- Star implementation of the new unfold function · 9b9eef59
  Eric Coissac committed Nov 05, 2016
  
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04 Nov, 2016 14 commits
- Remove fasta output redirection to a file · 48666605
  Eric Coissac committed Nov 04, 2016
  
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- Adds the logger to the scaffold call · 3ce945b3
  Eric Coissac committed Nov 04, 2016
  
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- Adds the logger to the scaffold call · 86341e86
  Eric Coissac committed Nov 04, 2016
  
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- Removes non useful imports · 219a4b08
  Eric Coissac committed Nov 04, 2016
  
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- Add the logger to the scaffold call · 85b7683b
  Eric Coissac committed Nov 04, 2016
  
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- Add the logger to the scaffold call · d682d89f
  Eric Coissac committed Nov 04, 2016
  
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- Add the logger to the scaffold call and modify for this the · 03cd4a59
```
`compactGraph2lastgraph` function
```
  Eric Coissac committed Nov 04, 2016
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- Add logger to the scafforld call · c80a94ef
  Eric Coissac committed Nov 04, 2016
  
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- Remove non useful import and add logger to the scaffold call · cfb160ee
  Eric Coissac committed Nov 04, 2016
  
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- Remove unuseful import · 0d8a1586
  Eric Coissac committed Nov 04, 2016
  
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- Patch logging from stderr to logger in scaffold · a4818eaf
  Eric Coissac committed Nov 04, 2016
  
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- Adds the stem id in the label of the scaffold edges · cf3897ec
  Eric Coissac committed Nov 04, 2016
  
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- Add a *class* key containing the value `scaffold:paired-end` to the · dde94122
```
edges added by the scaffold function on the base of the pair-ended links
```
  Eric Coissac committed Nov 04, 2016
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- Adds a *class* key to the compact assembly edges containing sequence · 46c64ffc
  Eric Coissac committed Nov 04, 2016
  
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03 Nov, 2016 4 commits
- Patch a bug in `selectGoodComponent` because of the new compact graph · bb765723
```
structure
```
  Eric Coissac committed Nov 03, 2016
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- Fix a bug in fillgap created by the change of API · f61e648a
  Eric Coissac committed Nov 03, 2016
  
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- Add a default length of 10 if estimated gap length is below zero · 53852200
  Eric Coissac committed Nov 03, 2016
  
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- Finalize the interface with the user · ec2c66d4
  Eric Coissac committed Nov 03, 2016
  
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02 Nov, 2016 3 commits
- remove warning in the code · bf597793
  Eric Coissac committed Nov 02, 2016
  
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- complete the graph compaction algorithm to provide more info · 1d469ab5
  Eric Coissac committed Nov 02, 2016
  
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- Add a new *graph* command to dump a graph file representing the · c4bacebe
```
assembling
```
  Eric Coissac committed Nov 02, 2016
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29 Sep, 2016 1 commit
- Change the variance formula to the variance estimator formula · 72601757
  Eric Coissac committed Sep 29, 2016
  
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27 Sep, 2016 1 commit
- Remove some error message related to cython syntax · 9e789f40
  Eric Coissac committed Sep 27, 2016
  
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06 Sep, 2016 1 commit
- switch to version 0.2.07 · 82b57e30
  Eric Coissac committed Sep 06, 2016
  
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16 Aug, 2016 1 commit
- Remove a wrong log on stdout · 5905d791
  Eric Coissac committed Aug 16, 2016
  
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03 Aug, 2016 2 commits
- Switch to version 0.2.06 · 4458150c
  Eric Coissac committed Aug 03, 2016
  
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- Patch a bug in the progressbar printing leading to a bus error with some · 25517945
```
C compiler and Cython version >+ 0.24
```
  Eric Coissac committed Aug 03, 2016
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29 Jul, 2016 1 commit
- Add a new `--maxfillgaps` option to limit the number of fillgaps cycle · 7b2d3ed8
```
and avoid infinite loop with some rare dataset
```
  Eric Coissac committed Jul 29, 2016
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03 Jul, 2016 5 commits
- Swithch to version 0.2.05 · cfa1d36c
  Eric Coissac committed Jul 03, 2016
  
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- changes a cdef to a cpdef · 1a7cd206
```
Signed-off-by: Eric Coissac <eric.coissac@metabarcoding.org>
```
  Eric Coissac committed Jul 03, 2016
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- Add code to manage the noprobe option · ea136ec4
```
Signed-off-by: Eric Coissac <eric.coissac@metabarcoding.org>
```
  Eric Coissac committed Jul 03, 2016
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- Adds a new default option · 262c9298
  Eric Coissac committed Jul 03, 2016
  
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- Substitutes fprintf call by fputs call to comply with the new Ubuntu · 9a593f02
```
compilation rules
```
  Eric Coissac committed Jul 03, 2016
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09 May, 2016 1 commit
- switch to version 0.2.04 · 32459077
  Eric Coissac committed May 09, 2016
  
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