Commits · master · OBITools / OBITools3

16 May, 2022 1 commit
- obi import: added SINTAX format import and switch to version 3.0.1b18 · ef9d9674
  mercierc authored May 17, 2022
  
  ef9d9674
02 May, 2022 2 commits
- switch to version 3.0.1b17 · 4f39bb24
  mercierc authored May 03, 2022
  
  4f39bb24
- import: added import of UNITE fasta format · 0a2b8adb
  mercierc authored May 03, 2022
  
  0a2b8adb
30 Mar, 2022 1 commit
- annotate: fixed a bug where a column type could be wrongly guessed and · f9b99a93
  mercierc authored Mar 30, 2022
```
switch to version 3.0.1b16
```
  f9b99a93
25 Feb, 2022 2 commits
- switch to version v3.0.1b15 · ce2833c0
  Celine Mercier authored Feb 25, 2022
  
  ce2833c0
- split command · f64b3da3
  Celine Mercier authored Feb 25, 2022
  
  f64b3da3
11 Nov, 2021 7 commits
- removed a trace · 388b3e04
  mercierc authored Nov 11, 2021
  
  388b3e04
- switch to version 3.0.1b14 · c9db990b
  mercierc authored Nov 11, 2021
  
  c9db990b
- Cython: View: fixed keys method to get list of view keys · 3f253feb
  mercierc authored Nov 11, 2021
  
  3f253feb
- small fix · 85d2bab6
  mercierc authored Nov 11, 2021
  
  85d2bab6
- small fixes and improvements · 53b3d811
  mercierc authored Nov 11, 2021
  
  53b3d811
- obi export: added options to export to metabaR compatible format · f6353fbf
  mercierc authored Nov 11, 2021
  
  f6353fbf
- goes with previous commit · 5a8b9dca
  mercierc authored Nov 11, 2021
  
  5a8b9dca
01 Nov, 2021 2 commits
- Python: URI decoding: now properly checking that paths can be encoded in · 8bd6d6c8
  mercierc authored Nov 02, 2021
```
ASCII (issue #89)
```
  8bd6d6c8
- Python: URI decoding: added metabaR output · 405e6ef4
  mercierc authored Nov 02, 2021
  
  405e6ef4
12 Sep, 2021 2 commits
- switch to version 3.0.1b13 · fedacfaf
  mercierc authored Sep 13, 2021
  
  fedacfaf
- python: genbank parser: better handling of white spaces · 2d66e0e9
  mercierc authored Sep 13, 2021
  
  2d66e0e9
07 Sep, 2021 4 commits
- switch to version 3.0.1b12 · f43856b7
  mercierc authored Sep 08, 2021
  
  f43856b7
- Cython: fixed rewriting of column when rewriting a 1 element dict column · 9e0c3198
  mercierc authored Sep 08, 2021
  
  9e0c3198
- C: views: now correctly parses view names containing '.' when cleaning · 58b42cd9
  mercierc authored Sep 08, 2021
```
unfinished views. Closes #115
```
  58b42cd9
- ngsfilter: checks better if there is an associated sequencing quality · 34de90bc
  mercierc authored Sep 08, 2021
  
  34de90bc
04 Aug, 2021 4 commits
- stats: fixed the computation of variance when it is equal to 0 · 4be9f36f
  mercierc authored Aug 05, 2021
  
  4be9f36f
- C: fixed the printing of view informations from a DMS (fixes #114 ) · f10e78ba
  mercierc authored Aug 05, 2021
  
  f10e78ba
- Cython: taxonomy: improved logging · 88c8463e
  mercierc authored Aug 05, 2021
  
  88c8463e
- ecopcr: now accepting taxonomy from a different DMS than the reference · 89168271
  mercierc authored Aug 05, 2021
```
sequences
```
  89168271
21 Jul, 2021 7 commits
- Switch to version 3.0.1b11 · 82d26420
  mercierc authored Jul 22, 2021
  
  82d26420
- export: now exports header for tabular files by default and added option · 99c1cd60
  mercierc authored Jul 22, 2021
```
to only export specific columns
```
  99c1cd60
- export: fixed 'only' option printing one too many if printing header · ce7ae4ac
  mercierc authored Jul 21, 2021
  
  ce7ae4ac
- cat: improved error handling · 0b4283bb
  mercierc authored Jul 21, 2021
  
  0b4283bb
- Improved taxonomy reading information display · 747f3efb
  mercierc authored Jul 21, 2021
  
  747f3efb
- Fixed the handling of sample names that are numbers (forcing conversion) · 6c1a3aff
  mercierc authored Jul 21, 2021
  
  6c1a3aff
- Implements #108 export integer missing values as 0 for tables by default · e2932b05
  mercierc authored Jul 21, 2021
  
  e2932b05
19 Jul, 2021 1 commit
- Addresses #111 · 32345b9e
  mercierc authored Jul 19, 2021
  
  32345b9e
16 Jun, 2021 1 commit
- import: improved genbank parser and switch to version 3.0.1.b10 · 9334cf6c
  mercierc authored Jun 17, 2021
  
  9334cf6c
31 May, 2021 6 commits
- Switch to version 3.0.1b9 · 8ec13a29
  mercierc authored Jun 01, 2021
  
  8ec13a29
- import: now imports and adds taxids for SILVA and RDP files, added · 3e45c344
  mercierc authored Jun 01, 2021
```
import of lists, fixed skipping of errors (was not overwriting), and
fixed --no-progress-bar option
```
  3e45c344
- build_ref_db: set default threshold to 0.99 · c2f3d90d
  mercierc authored Jun 01, 2021
  
  c2f3d90d
- align: fixed column URI parsing · 6b732d11
  mercierc authored Jun 01, 2021
  
  6b732d11
- typo fix · 9eb833a0
  mercierc authored Jun 01, 2021
  
  9eb833a0
- cat: fixed the handling of dictionary columns · 6b7b0e3b
  mercierc authored Jun 01, 2021
  
  6b7b0e3b