Commits · 7e50ffc152649b7d5254f1c4ca674270c789c4ee · ORG.Asm / ORG.Asm

09 Nov, 2016 3 commits
- First version of the new index command · 7e50ffc1
  Eric Coissac authored Nov 09, 2016
  
  7e50ffc1
- Add some cython optimisation flags · f8eac3bb
  Eric Coissac authored Nov 09, 2016
  
  f8eac3bb
- Add files and reads modules to deal with index checking more efficiently · 85ea5de9
  Eric Coissac authored Nov 09, 2016
  
  85ea5de9
07 Nov, 2016 9 commits
- Add a progress bar during automata construction · 6fa7d4cd
  Eric Coissac authored Nov 07, 2016
  
  6fa7d4cd
- Remove warnings · 8af6c6a7
  Eric Coissac authored Nov 07, 2016
  
  8af6c6a7
- ??? · 8c71a358
  Eric Coissac authored Nov 07, 2016
  
  8c71a358
- remove some warnings · ebcaba4f
  Eric Coissac authored Nov 07, 2016
  
  ebcaba4f
- import phiX174 · a323fb6a
  Eric Coissac authored Nov 07, 2016
  
  a323fb6a
- Remove a warning in the python editor · 1dbf873a
  Eric Coissac authored Nov 07, 2016
  
  1dbf873a
- Store phiX174 as another probe · b0c91cfa
  Eric Coissac authored Nov 07, 2016
  
  b0c91cfa
- Add config for the looking fo Phi X174 · 126a9ac0
  Eric Coissac authored Nov 07, 2016
  
  126a9ac0
- Add the phi x174 sequence in sample · bdd4c17e
  Eric Coissac authored Nov 07, 2016
  
  bdd4c17e
05 Nov, 2016 9 commits
- Fix #45 · 0758865d
  Eric Coissac authored Nov 05, 2016
  
  0758865d
- Fix #35 · 3ccff024
  Eric Coissac authored Nov 05, 2016
  
  3ccff024
- Fix the bug related to FIFO writing on macosx · 30ffb475
  Eric Coissac authored Nov 05, 2016
  
  30ffb475
- Change the rule to determine is probe sequences are proteins · 30b6f5a2
  Eric Coissac authored Nov 05, 2016
  
  30b6f5a2
- Supress the intermediate progression logging if the log is done on a tty · 5ab4154d
  Eric Coissac authored Nov 05, 2016
  
  5ab4154d
- Add the logger to the call to scaffold · be2c5ba6
  Eric Coissac authored Nov 05, 2016
  
  be2c5ba6
- Add a new assembler property to the compact assembly objects · 6c213599
  Eric Coissac authored Nov 05, 2016
  
  6c213599
- Change unfold command according to the new unfold algorithm · 80be8f89
  Eric Coissac authored Nov 05, 2016
  
  80be8f89
- Star implementation of the new unfold function · 9b9eef59
  Eric Coissac authored Nov 05, 2016
  
  9b9eef59
04 Nov, 2016 16 commits
- Remove fasta output redirection to a file · 48666605
  Eric Coissac authored Nov 04, 2016
  
  48666605
- Adds the logger to the scaffold call · 3ce945b3
  Eric Coissac authored Nov 04, 2016
  
  3ce945b3
- Adds the logger to the scaffold call · 86341e86
  Eric Coissac authored Nov 04, 2016
  
  86341e86
- Removes non useful imports · 219a4b08
  Eric Coissac authored Nov 04, 2016
  
  219a4b08
- Add the logger to the scaffold call · 85b7683b
  Eric Coissac authored Nov 04, 2016
  
  85b7683b
- Add the logger to the scaffold call · d682d89f
  Eric Coissac authored Nov 04, 2016
  
  d682d89f
- Add the logger to the scaffold call and modify for this the · 03cd4a59
  Eric Coissac authored Nov 04, 2016
```
`compactGraph2lastgraph` function
```
  03cd4a59
- Add logger to the scafforld call · c80a94ef
  Eric Coissac authored Nov 04, 2016
  
  c80a94ef
- Remove non useful import and add logger to the scaffold call · cfb160ee
  Eric Coissac authored Nov 04, 2016
  
  cfb160ee
- Remove unuseful import · 0d8a1586
  Eric Coissac authored Nov 04, 2016
  
  0d8a1586
- Patch logging from stderr to logger in scaffold · a4818eaf
  Eric Coissac authored Nov 04, 2016
  
  a4818eaf
- Adds the stem id in the label of the scaffold edges · cf3897ec
  Eric Coissac authored Nov 04, 2016
  
  cf3897ec
- Add a *class* key containing the value `scaffold:paired-end` to the · dde94122
  Eric Coissac authored Nov 04, 2016
```
edges added by the scaffold function on the base of the pair-ended links
```
  dde94122
- Adds a *class* key to the compact assembly edges containing sequence · 46c64ffc
  Eric Coissac authored Nov 04, 2016
  
  46c64ffc
- Change the cdhit command · d68dcb4c
  Eric Coissac authored Nov 04, 2016
  
  d68dcb4c
- Add data about plant barcodes · bfdf5e28
  Eric Coissac authored Nov 04, 2016
  
  bfdf5e28
03 Nov, 2016 3 commits
- Patch a bug in `selectGoodComponent` because of the new compact graph · bb765723
  Eric Coissac authored Nov 03, 2016
```
structure
```
  bb765723
- Fix a bug in fillgap created by the change of API · f61e648a
  Eric Coissac authored Nov 03, 2016
  
  f61e648a
- Add a default length of 10 if estimated gap length is below zero · 53852200
  Eric Coissac authored Nov 03, 2016
  
  53852200