Commits · master · OBITools / OBITools3 · GitLab

13 Jan, 2021 2 commits
- export: fixed a bug where exporting to tab format with a header would · 8ba7acdf
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not export the first line of data and switch to version 3.0.0b39
```
  Celine Mercier committed Jan 13, 2021
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- Removed spurious commentaries · 38051b1e
  Celine Mercier committed Jan 13, 2021
  
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06 Nov, 2020 1 commit
- grep: fixed `--id-list` option · 52a2e21b
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and switch to version 3.0.0b38
```
  Celine Mercier committed Nov 06, 2020
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30 Oct, 2020 6 commits
- Switch to version 3.0.0b37 · d27a5b91
  Celine Mercier committed Oct 30, 2020
  
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- New command: obi addtaxids to add NCBI taxids to sequences from their · 20bd3350
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taxon name.
```
  Celine Mercier committed Oct 30, 2020
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- Now handling sequences with Uracil (U) nucleotides by converting to · 2e191372
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Thymine (T)
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  Celine Mercier committed Oct 30, 2020
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- Taxonomy: new functions to find taxa by name · 112e12ca
  Celine Mercier committed Oct 30, 2020
  
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- import: now can import SILVA fasta files · b9b4cec5
  Celine Mercier committed Oct 30, 2020
  
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- Small fixes (potential compilation problems) · 199f3772
  Celine Mercier committed Oct 30, 2020
  
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29 Sep, 2020 2 commits
- ecotag: clarified similarity circle documentation · 422a6450
  Celine Mercier committed Sep 29, 2020
  
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- obi ls: now done in C (preparing things for R packages to read DMS) and · 137c109f
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switch to version 3.0.0b36
```
  Celine Mercier committed Sep 29, 2020
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25 Sep, 2020 3 commits
- Revert "Fixed version numbering mistake (should be b34 not b35)" · b6648ae8
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This reverts commit f6dffbec
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  Celine Mercier committed Sep 25, 2020
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- Fixed version numbering mistake (should be b34 not b35) · f6dffbec
  Celine Mercier committed Sep 25, 2020
  
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- ecotag: added separate threshold for minimum circle identity (and switch · c4696ac8
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to version 3.0.0b35
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  Celine Mercier committed Sep 25, 2020
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28 Aug, 2020 1 commit
- obi cat: fixed open file descriptor leak and switch to version 3.0.0b34 · 11a0945a
  Celine Mercier committed Aug 28, 2020
  
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27 Aug, 2020 1 commit
- obi cat: fixed a bug introduced in 3.0.0b28 and switch to version · f23c40c9
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3.0.0b33
```
  Celine Mercier committed Aug 27, 2020
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13 Aug, 2020 1 commit
- switch to version 3.0.0b32 · f99fc13b
  Celine Mercier committed Aug 13, 2020
  
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12 Aug, 2020 1 commit
- C: patch for failed creation of AVL with errno EEXIST · 1da6aac1
  Celine Mercier committed Aug 12, 2020
  
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31 Jul, 2020 1 commit
- export: now automatically sorts dictionary keys alphabetically for · 159803b4
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tab/csv output
```
  Celine Mercier committed Jul 31, 2020
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30 Jul, 2020 2 commits
- import: fixed entry count estimation when importing fastq files · 7dcbc340
  Celine Mercier committed Jul 30, 2020
  
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- uniq: added a check to make sure that there is more than one element for · db2202c8
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one tag when merging its information
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  Celine Mercier committed Jul 30, 2020
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28 Jul, 2020 2 commits
- switch to version 3.0.0b31 · d33ff978
  Celine Mercier committed Jul 28, 2020
  
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- export: fixed a bug introduced in version 3.0.0b28 · 1dcdf69f
  Celine Mercier committed Jul 28, 2020
  
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27 Jul, 2020 3 commits
- Python: added "date created" information in view representation · dec114ee
  Celine Mercier committed Jul 27, 2020
  
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- Python: added the OBITools3 version that generated the view in view · f3669105
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comments
```
  Celine Mercier committed Jul 27, 2020
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- alignpairedend: fixed division by 0 bug and switch to version 3.0.0b30 · f2aa5fcf
  Celine Mercier committed Jul 27, 2020
  
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26 Jul, 2020 5 commits
- switch to version 3.0.0b29 · bccb3e68
  Celine Mercier committed Jul 26, 2020
  
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- C: added a missing error check · f5a17bea
  Celine Mercier committed Jul 26, 2020
  
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- C and Cython: fixed and improved the associated columns system · e2850763
  Celine Mercier committed Jul 26, 2020
  
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- obi test: made less heavy to be faster · e6feac93
  Celine Mercier committed Jul 26, 2020
  
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- obi import: added --space-priority option to import a view line by line · 50b292b4
  Celine Mercier committed Jul 26, 2020
  
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24 Jul, 2020 4 commits
- switch to version 3.0.0b28 · 24a737aa
  Celine Mercier committed Jul 24, 2020
  
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- Python: made all commands handle output to buffer object (e.g. stdout) · 8aa455ad
  Celine Mercier committed Jul 24, 2020
  
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- Cython: View: new method to print a view to a buffer (e.g. stdout) · 46ca693c
  Celine Mercier committed Jul 24, 2020
  
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- Cython: progress bar: set default refresh rate to 5 seconds · 9a9afde1
  Celine Mercier committed Jul 24, 2020
  
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13 Jul, 2020 3 commits
- grep: now prints the number of entries grepped · 8dd403a1
  Celine Mercier committed Jul 13, 2020
  
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- alignpairedend: improved/fixed the output tags for the alignment score · 9672f01c
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and lengths. Removed minimum score option
```
  Celine Mercier committed Jul 13, 2020
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- ngsfilter: unidentified sequences are now stored untrimmed · ed9549ac
  Celine Mercier committed Jul 13, 2020
  
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07 Jul, 2020 2 commits
- Switch to version 3.0.0b27 · 9ace9989
  Celine Mercier committed Jul 07, 2020
  
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- C: AVL trees: fixed a bug where storing the difference between 2 crc64 · a3ebe5f1
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values in an int64 would mess trees up resulting in failed data
dereplication
```
  Celine Mercier committed Jul 07, 2020
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