Commits · master · OBITools / OBITools3 · GitLab

07 Jul, 2020 2 commits
- Switch to version 3.0.0b27 · 9ace9989
  Celine Mercier committed Jul 07, 2020
  
  9ace9989 Browse Files
- C: AVL trees: fixed a bug where storing the difference between 2 crc64 · a3ebe5f1
```
values in an int64 would mess trees up resulting in failed data
dereplication
```
  Celine Mercier committed Jul 07, 2020
  a3ebe5f1 Browse Files
03 Jul, 2020 1 commit
- obi uniq: quick fix for bug where some sequences are not correctly · 9100e148
```
dereplicated
```
  Celine Mercier committed Jul 03, 2020
  9100e148 Browse Files
01 Jul, 2020 2 commits
- small help documentation improvement · ccda0661
  Celine Mercier committed Jul 01, 2020
  
  ccda0661 Browse Files
- obi clean: fixed a memory bug, fixed the behaviour when no sample info, · aab59f22
```
and added checks warnings and error handling when sample info not
dereplicated
```
  Celine Mercier committed Jul 01, 2020
  aab59f22 Browse Files
17 Jun, 2020 5 commits
- switch to version 3.0.0b26 · ade1107b
  Celine Mercier committed Jun 17, 2020
  
  ade1107b Browse Files
- export: dictionaries are now formatted like in the original OBITools · 9c7d2440
```
when exporting in tabular format and tuple formatting is cleaner
```
  Celine Mercier committed Jun 17, 2020
  9c7d2440 Browse Files
- Cython: utils: added handling of tuples to bytes2str_object function · 03bc9915
  Celine Mercier committed Jun 17, 2020
  
  03bc9915 Browse Files
- Cython: Columns: added a keys() method that returns all element names · 24b1dab5
  Celine Mercier committed Jun 17, 2020
  
  24b1dab5 Browse Files
- ngsfilter: now setting 'reversed' tag to False instead of None when · 7593673f
```
false
```
  Celine Mercier committed Jun 17, 2020
  7593673f Browse Files
13 Jun, 2020 3 commits
- switch to version 3.0.0b25 · aa01236c
  Celine Mercier committed Jun 13, 2020
  
  aa01236c Browse Files
- C: made indexer opening/closing cleaner · 49b8810a
  Celine Mercier committed Jun 13, 2020
  
  49b8810a Browse Files
- ls: fixed an issue where big DMS couldn't be read by ls · 7a39df54
  Celine Mercier committed Jun 13, 2020
  
  7a39df54 Browse Files
10 Jun, 2020 4 commits
- switch to temporary version 3.0.0b24a · 09e483b0
  Celine Mercier committed Jun 10, 2020
  
  09e483b0 Browse Files
- uniq: now outputs an empty view if input view is empty instead of · 14a25791
```
displaying an error
```
  Celine Mercier committed Jun 10, 2020
  14a25791 Browse Files
- grep: now creating empty views instead of displaying an error when · 36a8aaa9
```
selecting on an unexisting column/tag
```
  Celine Mercier committed Jun 10, 2020
  36a8aaa9 Browse Files
- ngsfilter: made one of the tag error messages more accurate · a17eb445
  Celine Mercier committed Jun 10, 2020
  
  a17eb445 Browse Files
09 Jun, 2020 5 commits
- Switch to version 3.0.0b24 · e4a32788
  Celine Mercier committed Jun 09, 2020
  
  e4a32788 Browse Files
- Cython: View: fixed bash history display · 2442cc80
  Celine Mercier committed Jun 09, 2020
  
  2442cc80 Browse Files
- uniq: improved progress bar of second browsing · aa836b2a
  Celine Mercier committed Jun 09, 2020
  
  aa836b2a Browse Files
- C: fixed a bug where indexers referring to tuples of certain types were · 8776ce22
```
not properly closed and imported
```
  Celine Mercier committed Jun 09, 2020
  8776ce22 Browse Files
- ecotag: Added list of taxids for all best matches (closes #80 ) · 4aa772c4
  Celine Mercier committed Jun 09, 2020
  
  4aa772c4 Browse Files
05 Jun, 2020 3 commits
- version 3.0.0b23a · b0b96ac3
  Celine Mercier committed Jun 05, 2020
  
  b0b96ac3 Browse Files
- C: kmer alignment: fixed a bug where scores of 0 were at · 687e42ad
```
(0+kmer_length-1) (and now setting alignment direction to None if score
is 0
```
  Celine Mercier committed Jun 05, 2020
  687e42ad Browse Files
- alignpairedend: fixed a bug when rebuilding joined (unaligned) sequences · 5fbbb6d3
```
where only the forward sequence was kept
```
  Celine Mercier committed Jun 05, 2020
  5fbbb6d3 Browse Files
04 Jun, 2020 3 commits
- Switch to version 3.0.0b23 · 359a9fe2
  Celine Mercier committed Jun 04, 2020
  
  359a9fe2 Browse Files
- Python: correctly flagged some mandatory options as required · f9b6851f
  Celine Mercier committed Jun 04, 2020
  
  f9b6851f Browse Files
- Fixed installation on Ubuntu without pip · 29a2652b
  cmercier committed Jun 04, 2020
  
  29a2652b Browse Files
29 May, 2020 1 commit
- obi import: fixed a bug when skipping an entry · 2a2c2339
  Celine Mercier committed May 29, 2020
  
  2a2c2339 Browse Files
28 May, 2020 3 commits
- Switch to version 3.0.0b21 · faf8ea9d
  Celine Mercier committed May 28, 2020
  
  faf8ea9d Browse Files
- Genbank parser: now reading ORIGIN lines with comments without · ffe2485e
```
triggering error
```
  Celine Mercier committed May 28, 2020
  ffe2485e Browse Files
- obi import: skip on error more robust · 6094ce2b
  Celine Mercier committed May 28, 2020
  
  6094ce2b Browse Files
20 May, 2020 5 commits
- Minor changes for pip release · a7dcf16c
  Celine Mercier committed May 20, 2020
  
  a7dcf16c Browse Files
- obi import: minor doc/display improvements · f13f8f61
  Celine Mercier committed May 20, 2020
  
  f13f8f61 Browse Files
- Switch to version 3.0.0b19 · b5a29ac4
  Celine Mercier committed May 20, 2020
  
  b5a29ac4 Browse Files
- Cleaner installation · efd2b9d3
  Celine Mercier committed May 20, 2020
  
  efd2b9d3 Browse Files
- obi import: fixed to work with `seq` genbank extension · ca6e3e7a
  Celine Mercier committed May 20, 2020
  
  ca6e3e7a Browse Files
18 May, 2020 3 commits
- Switch to version 3.0.0b18 with version formatting that fits setuptools · 76ed8e18
  Celine Mercier committed May 18, 2020
  
  76ed8e18 Browse Files
- setup: now using setuptools instead of distutils to work with pip · 1d17f28a
  Celine Mercier committed May 18, 2020
  
  1d17f28a Browse Files
- obi import: small bug fix · fa834e4b
  Celine Mercier committed May 18, 2020
  
  fa834e4b Browse Files