Commits · efd2b9d338b907c4d9396394438eea2333cd3e2c · OBITools / OBITools3 · GitLab

20 May, 2020 2 commits
- Cleaner installation · efd2b9d3
  Celine Mercier authored May 20, 2020
  
  efd2b9d3
- obi import: fixed to work with `seq` genbank extension · ca6e3e7a
  Celine Mercier authored May 20, 2020
  
  ca6e3e7a
18 May, 2020 3 commits
- Switch to version 3.0.0b18 with version formatting that fits setuptools · 76ed8e18
  Celine Mercier authored May 18, 2020
  
  76ed8e18
- setup: now using setuptools instead of distutils to work with pip · 1d17f28a
  Celine Mercier authored May 18, 2020
  
  1d17f28a
- obi import: small bug fix · fa834e4b
  Celine Mercier authored May 18, 2020
  
  fa834e4b
12 May, 2020 1 commit
- Python: fasta parser: fixed a bug stopping the program when the last · a72fea3c
  Celine Mercier authored May 12, 2020
```
line contained a single nucleotide
```
  a72fea3c
07 May, 2020 6 commits
- Switch to version 3.0.0-beta16 · e9a37d8a
  Celine Mercier authored May 07, 2020
  
  e9a37d8a
- typo · ef074f84
  Celine Mercier authored May 07, 2020
  
  ef074f84
- C, views: no more automatic COUNT column if MERGED_sample column exists · aec5e69f
  Celine Mercier authored May 07, 2020
  
  aec5e69f
- Views: added obi prefix to commands in bash history · 170ef3f1
  Celine Mercier authored May 07, 2020
  
  170ef3f1
- obi uniq: fixed the remerging of already merged informations, and · f9999465
  Celine Mercier authored May 07, 2020
```
efficiency improvements
```
  f9999465
- obi import: fixed the import of old obitools files with premerged · 773b36ec
  Celine Mercier authored May 07, 2020
```
informations, and other minor improvements
```
  773b36ec
29 Apr, 2020 4 commits
- version 3.0.0-beta15c · 69cb434a
  Celine Mercier authored Apr 29, 2020
  
  69cb434a
- obi annotate: fixed annotation at ranks · 55d4f98d
  Celine Mercier authored Apr 29, 2020
  
  55d4f98d
- ecotag: fixed a bug where all the full DMS path weren't properly sent to · 0bec2631
  Celine Mercier authored Apr 29, 2020
```
the C layer
```
  0bec2631
- AVLs: Made an error message more informative · e6b6c6fa
  Celine Mercier authored Apr 29, 2020
  
  e6b6c6fa
28 Apr, 2020 2 commits
- build_ref_db: fixed bug erasing some of the higher LCAs (i.e. lowest · 974528b2
  Celine Mercier authored Apr 28, 2020
```
similarities)
```
  974528b2
- ecotag: better specificity by now correctly looking for similarities · 1b346b54
  Celine Mercier authored Apr 28, 2020
```
within refs above best score instead of ecotag threshold
```
  1b346b54
27 Apr, 2020 1 commit
- ecopcr: fixed a bug where sequences were considered circular (generating · 058f2ad8
  Celine Mercier authored Apr 27, 2020
```
false positives)
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  058f2ad8
24 Apr, 2020 1 commit
- obi annotate: now defaults to setting str if expression is not valid · 60bfd3ae
  Celine Mercier authored Apr 24, 2020
  
  60bfd3ae
18 Apr, 2020 2 commits
- C: build_ref_db: added progress display for each step · 67bdee10
  Celine Mercier authored Apr 18, 2020
  
  67bdee10
- C: Columns: optimizing column file growth · 0f745e01
  Celine Mercier authored Apr 18, 2020
  
  0f745e01
17 Apr, 2020 2 commits
- export: fixed progress bar bug · da8de52b
  cmercier authored Apr 17, 2020
  
  da8de52b
- C: SSE lcs alignment: band-aid for memory bug I don't understand · 4d36538c
  cmercier authored Apr 17, 2020
```
(triggered on specific db on ubuntu)
```
  4d36538c
15 Apr, 2020 2 commits
- Switch to version 3.0.0-beta14 · 8d0b17d8
  Celine Mercier authored Apr 15, 2020
  
  8d0b17d8
- Taxonomy: fixed a critical memory bug when building the list of merged · 343999a6
  Celine Mercier authored Apr 15, 2020
```
taxids
```
  343999a6
13 Apr, 2020 2 commits
- C: Columns: rounding column growth to ceil to avoid looping on small · e9a40630
  Celine Mercier authored Apr 13, 2020
```
values
```
  e9a40630
- C: Columns: reduced column growth factor from 2 to 1.3 to avoid errno28 · 8dbcd302
  Celine Mercier authored Apr 13, 2020
  
  8dbcd302
12 Apr, 2020 7 commits
- Switch to version 3.0.0-beta13 · 4cf635d0
  Celine Mercier authored Apr 12, 2020
  
  4cf635d0
- Made completion script cleaner · b7e7cc23
  Celine Mercier authored Apr 12, 2020
  
  b7e7cc23
- C: made error message more detailed when checking that sequences and · b6ab792c
  Celine Mercier authored Apr 12, 2020
```
qualities match
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  b6ab792c
- obi import: fixed inconsequential error when precomputing number of · ddea5a29
  Celine Mercier authored Apr 12, 2020
```
entries in some formats
```
  ddea5a29
- View bash history: removed useless shebang · 30852ab7
  Celine Mercier authored Apr 12, 2020
  
  30852ab7
- all commands (almost): cleaner DMS closing at the end · 4d029990
  Celine Mercier authored Apr 12, 2020
  
  4d029990
- obi stats: fixed error when printing bool keys · eef5156d
  Celine Mercier authored Apr 12, 2020
  
  eef5156d
10 Apr, 2020 2 commits
- goes with previous commit · e62c991b
  Celine Mercier authored Apr 10, 2020
  
  e62c991b
- ecopcr: now printing a warning instead of interrupting with an error · 1218eed7
  Celine Mercier authored Apr 10, 2020
```
when a taxid is not found
```
  1218eed7
09 Apr, 2020 2 commits
- obi import: fixed critical bug where the last entry of embl and genbank · cd9cea8c
  Celine Mercier authored Apr 09, 2020
```
files was not imported
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  cd9cea8c
- ecopcr: made some errors more informative · 98cfb70d
  Celine Mercier authored Apr 09, 2020
  
  98cfb70d
05 Apr, 2020 1 commit
- ecopcr: added warnings and check of primer length (related to #75 ) · b9f68c76
  Celine Mercier authored Apr 05, 2020
  
  b9f68c76