Commits · 073d98db087484107954f03477f280b9a3073fac · OBITools / OBITools3 · GitLab

31 Aug, 2019 3 commits
- C: ecotag: now prints a warning if the demanded threshold is lower than · 073d98db
```
the db threshold
```
  Celine Mercier committed Aug 31, 2019
  073d98db Browse Files
- C: build_ref_db: now adds a comment with the threshold used to build the · 0ee728c4
```
DB
```
  Celine Mercier committed Aug 31, 2019
  0ee728c4 Browse Files
- C: Json comments: added an obi_read_comment function to read one value · 7423baca
```
from comments
```
  Celine Mercier committed Aug 31, 2019
  7423baca Browse Files
29 Aug, 2019 7 commits
- Fixed log to be in str instead of bytes · 53dcbc8e
  Celine Mercier committed Aug 29, 2019
  
  53dcbc8e Browse Files
- obi import: fixed entry count · 4e75514b
  Celine Mercier committed Aug 29, 2019
  
  4e75514b Browse Files
- obi grep: made an error message clearer (error could be eventually be · 1ed2d45a
```
handled by program, looking for str in bytes returned by a column)
```
  Celine Mercier committed Aug 29, 2019
  1ed2d45a Browse Files
- C: optimized dir opening · e43e49d6
  Celine Mercier committed Aug 29, 2019
  
  e43e49d6 Browse Files
- Better detection of missing taxonomy · 18705302
  Celine Mercier committed Aug 29, 2019
  
  18705302 Browse Files
- Improved obi stats · dcf8cf1d
  Celine Mercier committed Aug 29, 2019
  
  dcf8cf1d Browse Files
- Improved progress display when importing files in a DMS · 3cfe3a9b
  Celine Mercier committed Aug 29, 2019
  
  3cfe3a9b Browse Files
28 Aug, 2019 1 commit
- Python: better display of tuple values in fasta format · 728af51c
  Celine Mercier committed Aug 28, 2019
  
  728af51c Browse Files
27 Aug, 2019 5 commits
- obi uniq: various improvements and fixes #66 · 99a397b8
  Celine Mercier committed Aug 27, 2019
  
  99a397b8 Browse Files
- C: fixed a memory bug in the array indexer · f5c472ff
  Celine Mercier committed Aug 27, 2019
  
  f5c472ff Browse Files
- minor comment · 580db2f7
  Celine Mercier committed Aug 27, 2019
  
  580db2f7 Browse Files
- Increased the threshold of elements per line in a column before they are · dbe09f83
```
stored as a character string
```
  Celine Mercier committed Aug 27, 2019
  dbe09f83 Browse Files
- Better handling of column lines with all values at NA · 3d1b2e8e
  Celine Mercier committed Aug 27, 2019
  
  3d1b2e8e Browse Files
19 Aug, 2019 1 commit
- fixes #61 : now reading merged taxids information when building a · ae5f42c2
```
reference database
```
  Celine Mercier committed Aug 19, 2019
  ae5f42c2 Browse Files
18 Aug, 2019 3 commits
- Fixed a bug where a directory was not closed properly resulting in errno · af7cecf5
```
24 sometimes
```
  Celine Mercier committed Aug 18, 2019
  af7cecf5 Browse Files
- Minor fixes · 5f20be44
  Celine Mercier committed Aug 18, 2019
  
  5f20be44 Browse Files
- Fixed a bug when sending a DMS path to a C function from Cython · 66441e0a
  Celine Mercier committed Aug 18, 2019
  
  66441e0a Browse Files
25 Jul, 2019 1 commit
- Fixed a bug where some commands wouldn't work if the input DMS was not · 13952358
```
in the current directory
```
  Celine Mercier committed Jul 25, 2019
  13952358 Browse Files
23 Jul, 2019 4 commits
- updated a comment · 9f38cd8c
  Celine Mercier committed Jul 23, 2019
  
  9f38cd8c Browse Files
- ecotag: fixed a bug where the wrong taxid for the best match was · 946f9723
```
retrieved
```
  Celine Mercier committed Jul 23, 2019
  946f9723 Browse Files
- embl parser: information display about progress when parsing multiple · 9752ff84
```
files
```
  Celine Mercier committed Jul 23, 2019
  9752ff84 Browse Files
- ngsfilter and alignpairedend: paired-end reads are now correctly · d99702f5
```
reversed and labeled to be aligned correctly by alignpairedend
```
  Celine Mercier committed Jul 23, 2019
  d99702f5 Browse Files
06 Jul, 2019 4 commits
- C: ecotag: fixed 2 memory bugs · 17593028
  Celine Mercier committed Jul 06, 2019
  
  17593028 Browse Files
- C: kmer similarity: small improvements · 86bfa96f
  Celine Mercier committed Jul 06, 2019
  
  86bfa96f Browse Files
- obi alignpairedend: fixed a bug where first seq was kept in result view · f765c6f4
```
instead of consensus seq
```
  Celine Mercier committed Jul 06, 2019
  f765c6f4 Browse Files
- obi stats: result display is now sorted · a83bf43a
  Celine Mercier committed Jul 06, 2019
  
  a83bf43a Browse Files
20 Jun, 2019 1 commit
- obiclean parallelized · 3d9f0352
  Celine Mercier committed Jun 20, 2019
  
  3d9f0352 Browse Files
19 Jun, 2019 1 commit
- multithreaded obiclean working but not cleaned · 9b4c3537
  Celine Mercier committed Jun 19, 2019
  
  9b4c3537 Browse Files
04 Jun, 2019 1 commit
- j loop with critical (untested) · fd0b7a91
  Celine Mercier committed Jun 04, 2019
  
  fd0b7a91 Browse Files
25 May, 2019 1 commit
- i loop parallelized: bad · debf59b2
  Celine Mercier committed May 25, 2019
  
  debf59b2 Browse Files
24 May, 2019 1 commit
- openmp on j loop (i loop probably better) · a04588da
  Celine Mercier committed May 24, 2019
  
  a04588da Browse Files
22 May, 2019 1 commit
- CMake: setting compiler higher to avoid conflicts, and linking libopenmp · ed5bb70c
  Celine Mercier committed May 22, 2019
  
  ed5bb70c Browse Files
19 May, 2019 1 commit
- obi clean: not using tsearch library anymore, a simple byte array · 22a5ae72
```
instead. A lot more time and memory efficient. Closes #67
```
  Celine Mercier committed May 19, 2019
  22a5ae72 Browse Files
12 Apr, 2019 2 commits
- Add a --cobitools3 options to setup.py · dc88181e
  Eric Coissac committed Apr 12, 2019
  
  dc88181e Browse Files
- Comment the install of the packages · 2f60e91d
  Eric Coissac committed Apr 12, 2019
  
  2f60e91d Browse Files
01 Apr, 2019 2 commits
- Ask for python 3.7 · 7ba27b6a
  Eric Coissac committed Apr 01, 2019
  
  7ba27b6a Browse Files
- Add the cmakefile to the manifest · d3937e10
  Eric Coissac committed Apr 01, 2019
  
  d3937e10 Browse Files