Commits · 50b292b48905ec91eeffcd323fd241830dd74983 · OBITools / OBITools3 · GitLab

26 Jul, 2020 1 commit
- 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
```
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
```
values in an int64 would mess trees up resulting in failed data
dereplication
```
  Celine Mercier committed Jul 07, 2020
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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
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01 Jul, 2020 2 commits
- small help documentation improvement · ccda0661
  Celine Mercier committed Jul 01, 2020
  
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- 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
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17 Jun, 2020 5 commits
- switch to version 3.0.0b26 · ade1107b
  Celine Mercier committed Jun 17, 2020
  
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- 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
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- Cython: utils: added handling of tuples to bytes2str_object function · 03bc9915
  Celine Mercier committed Jun 17, 2020
  
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- Cython: Columns: added a keys() method that returns all element names · 24b1dab5
  Celine Mercier committed Jun 17, 2020
  
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- ngsfilter: now setting 'reversed' tag to False instead of None when · 7593673f
```
false
```
  Celine Mercier committed Jun 17, 2020
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13 Jun, 2020 3 commits
- switch to version 3.0.0b25 · aa01236c
  Celine Mercier committed Jun 13, 2020
  
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- C: made indexer opening/closing cleaner · 49b8810a
  Celine Mercier committed Jun 13, 2020
  
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- ls: fixed an issue where big DMS couldn't be read by ls · 7a39df54
  Celine Mercier committed Jun 13, 2020
  
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10 Jun, 2020 4 commits
- switch to temporary version 3.0.0b24a · 09e483b0
  Celine Mercier committed Jun 10, 2020
  
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- uniq: now outputs an empty view if input view is empty instead of · 14a25791
```
displaying an error
```
  Celine Mercier committed Jun 10, 2020
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- grep: now creating empty views instead of displaying an error when · 36a8aaa9
```
selecting on an unexisting column/tag
```
  Celine Mercier committed Jun 10, 2020
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- ngsfilter: made one of the tag error messages more accurate · a17eb445
  Celine Mercier committed Jun 10, 2020
  
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09 Jun, 2020 5 commits
- Switch to version 3.0.0b24 · e4a32788
  Celine Mercier committed Jun 09, 2020
  
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- Cython: View: fixed bash history display · 2442cc80
  Celine Mercier committed Jun 09, 2020
  
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- uniq: improved progress bar of second browsing · aa836b2a
  Celine Mercier committed Jun 09, 2020
  
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- 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
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- ecotag: Added list of taxids for all best matches (closes #80 ) · 4aa772c4
  Celine Mercier committed Jun 09, 2020
  
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05 Jun, 2020 3 commits
- version 3.0.0b23a · b0b96ac3
  Celine Mercier committed Jun 05, 2020
  
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- 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
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- alignpairedend: fixed a bug when rebuilding joined (unaligned) sequences · 5fbbb6d3
```
where only the forward sequence was kept
```
  Celine Mercier committed Jun 05, 2020
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04 Jun, 2020 3 commits
- Switch to version 3.0.0b23 · 359a9fe2
  Celine Mercier committed Jun 04, 2020
  
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- Python: correctly flagged some mandatory options as required · f9b6851f
  Celine Mercier committed Jun 04, 2020
  
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- Fixed installation on Ubuntu without pip · 29a2652b
  cmercier committed Jun 04, 2020
  
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29 May, 2020 1 commit
- obi import: fixed a bug when skipping an entry · 2a2c2339
  Celine Mercier committed May 29, 2020
  
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28 May, 2020 3 commits
- Switch to version 3.0.0b21 · faf8ea9d
  Celine Mercier committed May 28, 2020
  
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- Genbank parser: now reading ORIGIN lines with comments without · ffe2485e
```
triggering error
```
  Celine Mercier committed May 28, 2020
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- obi import: skip on error more robust · 6094ce2b
  Celine Mercier committed May 28, 2020
  
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