Commits · a04588da31d962515ce827ec2ad8dd1ceef52efd · OBITools / OBITools3

24 May, 2019 1 commit
- openmp on j loop (i loop probably better) · a04588da
  Celine Mercier authored May 24, 2019
  
  a04588da
22 May, 2019 1 commit
- CMake: setting compiler higher to avoid conflicts, and linking libopenmp · ed5bb70c
  Celine Mercier authored May 22, 2019
  
  ed5bb70c
19 May, 2019 1 commit
- obi clean: not using tsearch library anymore, a simple byte array · 22a5ae72
  Celine Mercier authored May 19, 2019
```
instead. A lot more time and memory efficient. Closes #67
```
  22a5ae72
31 Mar, 2019 3 commits
- CMake: made required version 3.10 for ubuntu · 3afbbeb7
  Celine Mercier authored Mar 31, 2019
  
  3afbbeb7
- C: obi lcs: cleaner progress print · 7f8d1e71
  Celine Mercier authored Mar 31, 2019
  
  7f8d1e71
- C: made build_ref_db cleaner · 26fb149e
  Celine Mercier authored Mar 31, 2019
  
  26fb149e
30 Mar, 2019 5 commits
- Removing trace · f0ff5854
  Celine Mercier authored Mar 30, 2019
  
  f0ff5854
- C: Views: fixed a bug when creating automatic columns with unformatted · 7c518300
  Celine Mercier authored Mar 30, 2019
```
comments
```
  7c518300
- C: taxonomy: fixed a segfault on linux when trying to fclose an unopened · 52b3a9fc
  Celine Mercier authored Mar 30, 2019
```
file
```
  52b3a9fc
- fixed typo · 0847d618
  Celine Mercier authored Mar 30, 2019
  
  0847d618
- C: build_reference_db: made some errors more explicit · 9fcebd76
  Celine Mercier authored Mar 30, 2019
  
  9fcebd76
29 Mar, 2019 4 commits
- Cleaning first stage · cdd5975e
  Eric Coissac authored Mar 29, 2019
  
  cdd5975e
- Add some .ignore files · bf62960e
  Eric Coissac authored Mar 29, 2019
  
  bf62960e
- Add the location of install · 52b8008b
  Eric Coissac authored Mar 29, 2019
  
  52b8008b
- alignpairedend: fixed the worst memory leak and the handling of the case · ee994721
  Celine Mercier authored Mar 29, 2019
```
where 0 common kmers are found
```
  ee994721
26 Mar, 2019 1 commit
- First version of the simplified setup.py script · 10ab5572
  Eric Coissac authored Mar 26, 2019
  
  10ab5572
13 Mar, 2019 1 commit
- added math.h import where needed · 50e7cd61
  Celine Mercier authored Mar 13, 2019
  
  50e7cd61
07 Mar, 2019 1 commit
- Fixed a bug when creating a column and checking the comments string if · 1ee50b72
  Celine Mercier authored Mar 07, 2019
```
it was NULL
```
  1ee50b72
17 Feb, 2019 1 commit
- Fixed the new alignpaired end to work after ngsfilter with the 9879847 · e026e9ec
  Celine Mercier authored Feb 17, 2019
```
possible cases
```
  e026e9ec
10 Feb, 2019 1 commit
- Fixed a bug in kmer similarity computation where the fact that sequences · 30153105
  Celine Mercier authored Feb 10, 2019
```
could be switched was not accounted for
```
  30153105
06 Feb, 2019 1 commit
- ecoPCR: fixed amplicon length computation bug · 6ca6d27e
  Celine Mercier authored Feb 06, 2019
  
  6ca6d27e
21 Jan, 2019 4 commits
- Various commentaries and insignificant fixes · 0b62619e
  Celine Mercier authored Jan 21, 2019
  
  0b62619e
- Alignpairedend: added alignment using shifting with best kmer similarity · c7f5b8d9
  Celine Mercier authored Jan 21, 2019
```
(low level layer in C and Cython API)
```
  c7f5b8d9
- C: taxonomy: fixed a bug when checking for root node · 59017c0d
  Celine Mercier authored Jan 21, 2019
  
  59017c0d
- C: Added a function to get a nucleotide at a specific index in an · 9f6bba18
  Celine Mercier authored Jan 21, 2019
```
encoded sequence
```
  9f6bba18
09 Dec, 2018 6 commits
- New command and C functions: obi ecotag · eb586b2f
  Celine Mercier authored Dec 09, 2018
  
  eb586b2f
- C obi_lcs: updated deprecated column names and associated comments · 9556130b
  Celine Mercier authored Dec 09, 2018
  
  9556130b
- C obi_lcs: fixed checking for identical sequences when aligning 2 · 005aaeec
  Celine Mercier authored Dec 09, 2018
```
columns
```
  005aaeec
- C alignment filter: added a check for sequences not being equal when the · da445066
  Celine Mercier authored Dec 09, 2018
```
threshold requires that they are
```
  da445066
- C Views: made an error message more specific · 0a407436
  Celine Mercier authored Dec 09, 2018
  
  0a407436
- C build ref db: fixed 2 bugs when setting arrays: size of an element in · 54efff36
  Celine Mercier authored Dec 09, 2018
```
in bits not bytes and using view API instead of column API
```
  54efff36
27 Nov, 2018 5 commits
- C, views: made 'view_exists' function public (now 'obi_view_exists') · 12087a6c
  Celine Mercier authored Nov 27, 2018
  
  12087a6c
- Fixed a bug in the array indexer where the value's length was no · fbabbceb
  Celine Mercier authored Nov 27, 2018
```
properly set to 0 if the value was NA (ignore previous commit with the
same message)
```
  fbabbceb
- Fixed a bug in the array indexer where the value's length was not · b3bfa9ca
  Celine Mercier authored Nov 27, 2018
```
properly set to 0 if the value was NA
```
  b3bfa9ca
- C, taxonomy: new function to get the lowest common ancestor of two taxa · ef8dc85f
  Celine Mercier authored Nov 27, 2018
  
  ef8dc85f
- C: new function to build a reference database with LCA and score · f942dd85
  Celine Mercier authored Nov 27, 2018
```
metadata for the taxonomic assignment of sequences
```
  f942dd85
19 Nov, 2018 4 commits
- minor fixes and comments · 730ea99f
  Celine Mercier authored Nov 19, 2018
  
  730ea99f
- AVLs: made maximum number of nodes per AVL 5 millions, as this combined · e9c1d5e4
  Celine Mercier authored Nov 19, 2018
```
with keeping all AVLs mapped seems the most efficient. Now 1 million
sequences more or less constantly takes 1 minute.
```
  e9c1d5e4
- AVLs: AVLs in a group are not unmapped and remapped constantly anymore · 7fc1b578
  Celine Mercier authored Nov 19, 2018
```
when adding new values, fixed a bug when calculating if an AVL data file
has reached the maximum size, fixed a casting bug, and added a boolean
so read-only AVLs files are not truncated
```
  7fc1b578
- Fixed 2 bugs when checking qualities matching sequences predicate: now · 31053591
  Celine Mercier authored Nov 19, 2018
```
closing and reopening indexers so that they are mapped properly, and
fixed memory leak when reading sequences
```
  31053591