obitools/obitools3
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 66 Wiki Activity

Commit Graph

  • e43e49d6f1 C: optimized dir opening Celine Mercier 2019-08-29 16:35:10 +02:00
  • 187053026f Better detection of missing taxonomy Celine Mercier 2019-08-29 16:10:09 +02:00
  • dcf8cf1d64 Improved obi stats Celine Mercier 2019-08-29 15:18:26 +02:00
  • 3cfe3a9b00 Improved progress display when importing files in a DMS Celine Mercier 2019-08-29 10:12:06 +02:00
  • 728af51cb2 Python: better display of tuple values in fasta format Celine Mercier 2019-08-28 15:55:36 +02:00
  • 99a397b842 obi uniq: various improvements and fixes #66 Celine Mercier 2019-08-27 20:27:36 +02:00
  • f5c472ffd1 C: fixed a memory bug in the array indexer Celine Mercier 2019-08-27 20:26:46 +02:00
  • 580db2f710 minor comment Celine Mercier 2019-08-27 20:25:54 +02:00
  • dbe09f83a2 Increased the threshold of elements per line in a column before they are stored as a character string Celine Mercier 2019-08-27 20:25:14 +02:00
  • 3d1b2e8ed9 Better handling of column lines with all values at NA Celine Mercier 2019-08-27 20:20:26 +02:00
  • ae5f42c260 fixes #61 : now reading merged taxids information when building a reference database Celine Mercier 2019-08-19 12:30:56 +02:00
  • af7cecf59f Fixed a bug where a directory was not closed properly resulting in errno 24 sometimes Celine Mercier 2019-08-18 19:46:52 +02:00
  • 5f20be44b2 Minor fixes Celine Mercier 2019-08-18 19:45:53 +02:00
  • 66441e0aef Fixed a bug when sending a DMS path to a C function from Cython Celine Mercier 2019-08-18 19:43:51 +02:00
  • 13952358b3 Fixed a bug where some commands wouldn't work if the input DMS was not in the current directory Celine Mercier 2019-07-25 11:59:19 +02:00
  • 9f38cd8cf6 updated a comment Celine Mercier 2019-07-23 19:03:24 +02:00
  • 946f9723b8 ecotag: fixed a bug where the wrong taxid for the best match was retrieved Celine Mercier 2019-07-23 19:02:17 +02:00
  • 9752ff8494 embl parser: information display about progress when parsing multiple files Celine Mercier 2019-07-23 18:59:07 +02:00
  • d99702f56f ngsfilter and alignpairedend: paired-end reads are now correctly reversed and labeled to be aligned correctly by alignpairedend Celine Mercier 2019-07-23 18:56:51 +02:00
  • 1759302829 C: ecotag: fixed 2 memory bugs Celine Mercier 2019-07-06 16:31:19 +02:00
  • 86bfa96fbe C: kmer similarity: small improvements Celine Mercier 2019-07-06 16:30:32 +02:00
  • f765c6f41e obi alignpairedend: fixed a bug where first seq was kept in result view instead of consensus seq Celine Mercier 2019-07-06 16:29:32 +02:00
  • a83bf43ab9 obi stats: result display is now sorted Celine Mercier 2019-07-06 16:27:51 +02:00
  • 3d9f0352ff obiclean parallelized Celine Mercier 2019-06-20 19:44:04 +02:00
  • 9b4c3537f9 multithreaded obiclean working but not cleaned Celine Mercier 2019-06-19 17:29:58 +02:00
  • fd0b7a9177 j loop with critical (untested) Celine Mercier 2019-06-04 17:14:36 +02:00
  • debf59b266 i loop parallelized: bad Celine Mercier 2019-05-25 18:37:56 +02:00
  • a04588da31 openmp on j loop (i loop probably better) Celine Mercier 2019-05-24 16:51:04 +02:00
  • ed5bb70c80 CMake: setting compiler higher to avoid conflicts, and linking libopenmp Celine Mercier 2019-05-22 16:26:30 +02:00
  • 22a5ae72d1 obi clean: not using tsearch library anymore, a simple byte array instead. A lot more time and memory efficient. Closes #67 Celine Mercier 2019-05-19 17:39:53 +02:00
  • dc88181eeb Add a --cobitools3 options to setup.py Eric Coissac 2019-04-12 14:55:05 +02:00
  • 2f60e91d93 Comment the install of the packages Eric Coissac 2019-04-12 13:03:53 +02:00
  • 7ba27b6a99 Ask for python 3.7 Eric Coissac 2019-04-01 09:08:27 +02:00
  • d3937e1051 Add the cmakefile to the manifest Eric Coissac 2019-04-01 09:01:45 +02:00
  • 35eeb07f08 Build the C src in build/cobject Eric Coissac 2019-04-01 08:52:38 +02:00
  • 3afbbeb7e5 CMake: made required version 3.10 for ubuntu Celine Mercier 2019-03-31 16:54:05 +02:00
  • d6056a8e50 dirty temporary fix for install Celine Mercier 2019-03-31 16:19:05 +02:00
  • ac47bdce5d history: fixed DMS history when multiple inputs Celine Mercier 2019-03-31 15:44:20 +02:00
  • 7f8d1e7196 C: obi lcs: cleaner progress print Celine Mercier 2019-03-31 15:42:58 +02:00
  • 80068a3c19 ngsfilter: fixed parsing error Celine Mercier 2019-03-31 15:42:30 +02:00
  • a3e6b7d913 obi import: fixed import of View_NUC_SEQS to another DMS Celine Mercier 2019-03-31 15:42:07 +02:00
  • 416c2d7ba0 Cython: made fasta formatter cleaner Celine Mercier 2019-03-31 15:41:32 +02:00
  • 26fb149efb C: made build_ref_db cleaner Celine Mercier 2019-03-31 15:40:13 +02:00
  • 2b8c066f8e Cython: added possibility to output in tabular format Celine Mercier 2019-03-31 15:39:38 +02:00
  • e39c1a7fbf Cython: added tab formatter and parser (for obi export) Celine Mercier 2019-03-31 15:38:34 +02:00
  • 6841d879aa obi history: fixed a bug when displaying ascii history Celine Mercier 2019-03-31 10:51:52 +02:00
  • f0ff585455 Removing trace Celine Mercier 2019-03-30 20:52:54 +01:00
  • 601a2cfd7d obi uniq: various fixes... Celine Mercier 2019-03-30 20:34:53 +01:00
  • 7c518300a0 C: Views: fixed a bug when creating automatic columns with unformatted comments Celine Mercier 2019-03-30 20:33:14 +01:00
  • f16bbca8e2 obi grep: fixed a bug where -p option didn't work Celine Mercier 2019-03-30 19:10:42 +01:00
  • 173483448a Merge commit '3d842ff7' Celine Mercier 2019-03-30 15:29:52 +01:00
  • 52b3a9fc39 C: taxonomy: fixed a segfault on linux when trying to fclose an unopened file Celine Mercier 2019-03-30 15:19:12 +01:00
  • ce686e9569 obi import: progress bar fixed when using --only option Celine Mercier 2019-03-30 15:16:57 +01:00
  • c293cfabbb Python: embl parser: fixed a bug preventing taxids from being parsed Celine Mercier 2019-03-30 15:15:49 +01:00
  • 0847d618d6 fixed typo Celine Mercier 2019-03-30 15:14:30 +01:00
  • 9fcebd7643 C: build_reference_db: made some errors more explicit Celine Mercier 2019-03-30 15:11:49 +01:00
  • 5d842ff7e7 Clean the manifest of old files Eric Coissac 2019-03-29 16:58:45 +01:00
  • 3445579251 remove all the no more needed .cfiles Eric Coissac 2019-03-29 16:56:58 +01:00
  • 995a66b488 Add the new script emplacement Eric Coissac 2019-03-29 16:55:23 +01:00
  • 5007b02cbc cleaning stage 2 Eric Coissac 2019-03-29 16:46:17 +01:00
  • cdd5975e8b Cleaning first stage Eric Coissac 2019-03-29 16:40:36 +01:00
  • 0c466046f4 Merge branch 'pip-standard-orig-python' into 'master' Eric Coissac 2019-03-29 16:25:01 +01:00
  • 2774422224 Patch the way of installing the obi main command pip-standard-orig-python Eric Coissac 2019-03-29 16:21:28 +01:00
  • bf62960ee8 Add some .ignore files Eric Coissac 2019-03-29 15:52:54 +01:00
  • 9c41b1e9da Move and rename the obi.py script Eric Coissac 2019-03-29 15:45:38 +01:00
  • 3a6d1be795 remove the old distutils Eric Coissac 2019-03-29 15:42:45 +01:00
  • 6c52966033 Switch back to the original python source from the paster branch Eric Coissac 2019-03-29 15:24:31 +01:00
  • 460187970f First version compiling the code correctly Eric Coissac 2019-03-29 15:22:10 +01:00
  • 52b8008bdc Add the location of install Eric Coissac 2019-03-29 15:21:30 +01:00
  • 6b9da38087 patch some relative imports Eric Coissac 2019-03-29 15:19:44 +01:00
  • ee9947217c alignpairedend: fixed the worst memory leak and the handling of the case where 0 common kmers are found Celine Mercier 2019-03-29 11:16:25 +01:00
  • ceaafca427 ngsfilter: fixed a bug (maybe 2) in the algo for the choice of the reverse primer when running on unaligned sequences Celine Mercier 2019-03-29 10:56:17 +01:00
  • 7c2787b6b3 trying to fix cython difficulties pip-standard Celine Mercier 2019-03-26 16:19:55 +01:00
  • 14eca43eac Import taxo Eric Coissac 2019-03-26 16:17:44 +01:00
  • 0b4ea49539 Convert relative import an delete cfiles Eric Coissac 2019-03-26 16:14:03 +01:00
  • cd88c37a7e Merge branch 'pip-standard' of git@git.metabarcoding.org:obitools/obitools3.git into pip-standard Eric Coissac 2019-03-26 15:54:49 +01:00
  • 1095a617a3 Patch relative import to absolute Eric Coissac 2019-03-26 15:54:33 +01:00
  • 5a05258fcb fixed relative cython imports to be absolute Celine Mercier 2019-03-26 15:52:59 +01:00
  • 10ab557259 First version of the simplified setup.py script Eric Coissac 2019-03-26 15:40:31 +01:00
  • 8e70bf1ee1 obi import: fixed bug when rewriting a column (keeping wrong type in import module) Celine Mercier 2019-03-26 14:56:18 +01:00
  • d8a7bd42bd Cython API, taxonomy: fixed parental tree iterator (skipped second to last taxon, in OBI1 too) Celine Mercier 2019-03-26 14:08:54 +01:00
  • 06178d9d61 Genbank file parser functions that should have been included in a previous commit Celine Mercier 2019-03-20 11:44:43 +01:00
  • 3abe1b7ace obi_errno_to_exception function now properly reads obi_errno global variable directly Celine Mercier 2019-03-20 11:43:12 +01:00
  • 802a3f5933 data import: entries now counted if there are multiple files Celine Mercier 2019-03-18 18:16:39 +01:00
  • 7e20870719 Added genbank parser Celine Mercier 2019-03-15 16:06:27 +01:00
  • e8090a44c9 Fixed the ultimate bug with embl (and genbank) parsers: raising any exception in a python generator makes it unable to resume. So now, exceptions are not raised but printed, then functions return None and that's handled at higher level. Celine Mercier 2019-03-15 16:06:06 +01:00
  • 832f582802 Fixed no-skip-on-error option :p Celine Mercier 2019-03-15 16:04:04 +01:00
  • 58d0c850c2 Made skip on error option True by default...... Celine Mercier 2019-03-15 15:50:40 +01:00
  • 7737211ac2 Small fix in embl and genbank features parser Celine Mercier 2019-03-15 15:50:11 +01:00
  • c953f0cb00 Fixed embl import where sequences were not imported as Nuc_Seq objects Celine Mercier 2019-03-15 11:41:07 +01:00
  • bb045c3ae9 added TAXID_COLUMN to C API declarations for Cython Celine Mercier 2019-03-15 11:40:06 +01:00
  • 2a4f1b8feb obi import: now properly uses macros for column names Celine Mercier 2019-03-15 11:39:21 +01:00
  • 24a63f8732 URIs: URIs built with autocomplete now work too Celine Mercier 2019-03-15 10:52:27 +01:00
  • 478d19ab43 Cleaner stderr prints Celine Mercier 2019-03-13 18:36:31 +01:00
  • e3c565d6be Cleaner progress bar Celine Mercier 2019-03-13 18:36:05 +01:00
  • d88390c6d8 Cython API: when importing a file in a DMS, its length is computed beforehand for the progress bar Celine Mercier 2019-03-13 18:35:32 +01:00
  • 50e7cd61a6 added math.h import where needed Celine Mercier 2019-03-13 11:17:25 +01:00
  • 49d5f6fb1e removed deprecated comment Celine Mercier 2019-03-13 11:17:04 +01:00
  • b45c2ee653 Cython API: cleaner column rewriting API Celine Mercier 2019-03-13 11:13:55 +01:00
  • 6afd1294a7 Cython API: Views: fixed a bug when rewriting a column with different attributes (last line is not written anymore) Celine Mercier 2019-03-12 16:40:30 +01:00