Commits · master · OBITools / OBITools3 · GitLab

19 Feb, 2019 4 commits
- Update distutils for openmp and new version of pip · 52de6f27
  Eric Coissac committed Feb 19, 2019
  
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- Add cfiles everywhere ;-) · 29c56572
  Eric Coissac committed Feb 19, 2019
  
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- Renamed CAPI file · de3d12af
  Celine Mercier committed Feb 19, 2019
  
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- better cfiles · 9ccddd52
  Celine Mercier committed Feb 19, 2019
  
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17 Feb, 2019 1 commit
- Fixed the new alignpaired end to work after ngsfilter with the 9879847 · e026e9ec
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possible cases
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  Celine Mercier committed Feb 17, 2019
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12 Feb, 2019 1 commit
- embl iterator: only option on embl directories now works as intended · 4ddd1a1c
  Celine Mercier committed Feb 12, 2019
  
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10 Feb, 2019 1 commit
- Fixed a bug in kmer similarity computation where the fact that sequences · 30153105
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could be switched was not accounted for
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  Celine Mercier committed Feb 10, 2019
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06 Feb, 2019 4 commits
- ngsfilter: reworked to use apat library · 08bcbcd3
  Celine Mercier committed Feb 06, 2019
  
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- Cython API: added API to use apat (pattern search) C library · 04a36823
  Celine Mercier committed Feb 06, 2019
  
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- ecoPCR: fixed amplicon length computation bug · 6ca6d27e
  Celine Mercier committed Feb 06, 2019
  
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- Cython API: changed revcomp attribute of Nuc_Seq class to is_revcomp to · 8f189075
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be more explicit
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  Celine Mercier committed Feb 06, 2019
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21 Jan, 2019 4 commits
- Various commentaries and insignificant fixes · 0b62619e
  Celine Mercier committed Jan 21, 2019
  
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- Alignpairedend: added alignment using shifting with best kmer similarity · c7f5b8d9
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(low level layer in C and Cython API)
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  Celine Mercier committed Jan 21, 2019
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- C: taxonomy: fixed a bug when checking for root node · 59017c0d
  Celine Mercier committed Jan 21, 2019
  
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- C: Added a function to get a nucleotide at a specific index in an · 9f6bba18
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encoded sequence
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  Celine Mercier committed Jan 21, 2019
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11 Dec, 2018 1 commit
- obi import: fixed writing quality in views when appropriate (but still · 2a6a112d
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not a satisfying solution)
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  Celine Mercier committed Dec 11, 2018
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10 Dec, 2018 1 commit
- Cython: fixed history dot graph for all views, and fixed history · c437931a
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recording for build_ref_db and ecotag
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  Celine Mercier committed Dec 10, 2018
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09 Dec, 2018 8 commits
- New command and C functions: obi ecotag · eb586b2f
  Celine Mercier committed Dec 09, 2018
  
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- C obi_lcs: updated deprecated column names and associated comments · 9556130b
  Celine Mercier committed Dec 09, 2018
  
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- C obi_lcs: fixed checking for identical sequences when aligning 2 · 005aaeec
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columns
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  Celine Mercier committed Dec 09, 2018
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- obi align (pouic): fixed bug with the saved config when aligning 2 · 579f56bb
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different views
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  Celine Mercier committed Dec 09, 2018
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- C alignment filter: added a check for sequences not being equal when the · da445066
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threshold requires that they are
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  Celine Mercier committed Dec 09, 2018
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- C Views: made an error message more specific · 0a407436
  Celine Mercier committed Dec 09, 2018
  
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- C build ref db: fixed 2 bugs when setting arrays: size of an element in · 54efff36
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in bits not bytes and using view API instead of column API
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  Celine Mercier committed Dec 09, 2018
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- Missing commit for build_ref_db: C API file for cython · 6acb2171
  Celine Mercier committed Dec 09, 2018
  
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27 Nov, 2018 7 commits
- C, views: made 'view_exists' function public (now 'obi_view_exists') · 12087a6c
  Celine Mercier committed Nov 27, 2018
  
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- Fixed a bug in the array indexer where the value's length was no · fbabbceb
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properly set to 0 if the value was NA (ignore previous commit with the
same message)
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  Celine Mercier committed Nov 27, 2018
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- Cython: fxed a bug in INT tuple columns where values were converted to · 6f27734d
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double instead of int
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  Celine Mercier committed Nov 27, 2018
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- Fixed a bug in the array indexer where the value's length was not · b3bfa9ca
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properly set to 0 if the value was NA
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  Celine Mercier committed Nov 27, 2018
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- new command: build_ref_db to build a reference database with metadata · ece942e7
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for the taxonomic assignment of sequences
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  Celine Mercier committed Nov 27, 2018
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- C, taxonomy: new function to get the lowest common ancestor of two taxa · ef8dc85f
  Celine Mercier committed Nov 27, 2018
  
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- C: new function to build a reference database with LCA and score · f942dd85
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metadata for the taxonomic assignment of sequences
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  Celine Mercier committed Nov 27, 2018
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19 Nov, 2018 5 commits
- minor fixes and comments · 730ea99f
  Celine Mercier committed Nov 19, 2018
  
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- obi import: better checking of whether to import quality · 4d51f4f0
  Celine Mercier committed Nov 19, 2018
  
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- AVLs: made maximum number of nodes per AVL 5 millions, as this combined · e9c1d5e4
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with keeping all AVLs mapped seems the most efficient. Now 1 million
sequences more or less constantly takes 1 minute.
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  Celine Mercier committed Nov 19, 2018
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- AVLs: AVLs in a group are not unmapped and remapped constantly anymore · 7fc1b578
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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
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  Celine Mercier committed Nov 19, 2018
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- Fixed 2 bugs when checking qualities matching sequences predicate: now · 31053591
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closing and reopening indexers so that they are mapped properly, and
fixed memory leak when reading sequences
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  Celine Mercier committed Nov 19, 2018
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07 Nov, 2018 3 commits
- New command: obi align, except it's called obi pouic for now because of · b0da36cb
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a Cython compilation bug
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  Celine Mercier committed Nov 07, 2018
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- Minor fixes · d1f1fd43
  Celine Mercier committed Nov 07, 2018
  
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- Renamed Cython alignment library in an attempt to limit some compilation · 75a28929
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bugs potentially involving name conflicts
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  Celine Mercier committed Nov 07, 2018
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