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  • 0dfd67ec89 The endianness of binary taxonomy files is now correctly checked Celine Mercier 2016-10-10 17:04:29 +02:00
  • 0faaac49cf The taxonomy directory of the DMS is now automatically created with the DMS Celine Mercier 2016-10-10 17:02:51 +02:00
  • 1b07109e51 Removed deprecated code Celine Mercier 2016-10-10 17:01:51 +02:00
  • 60ab503a14 Added properties in the OBI_Taxonomy class Celine Mercier 2016-10-10 17:01:17 +02:00
  • 2dcfdc59fc When a new view is created with a line selection, the view to clone is automatically found + compacted redundant code + fixed potential bug when cloning a NUC_SEQS view by name Celine Mercier 2016-10-06 17:55:18 +02:00
  • 399fc2c051 Removed deprecated source files previously used for tests Celine Mercier 2016-09-30 17:49:37 +02:00
  • 9cd57deca9 Added OBIView_line_selection class to make new line selections associated with the view to clone, and improved and renamed method closing a view Celine Mercier 2016-09-30 17:48:53 +02:00
  • d88811ed7d Added a seed option to the obi test command for reproducible tests Celine Mercier 2016-09-29 17:34:48 +02:00
  • 8c402101e4 Renamed private attributes as _* and removed some deprecated code Celine Mercier 2016-09-28 16:56:44 +02:00
  • 1a7b42018e Added some error checking when opening or creating a view Celine Mercier 2016-09-28 14:28:34 +02:00
  • b717e8bb8b Added properties for the OBIView class and cleaned up deprecated code Celine Mercier 2016-09-28 14:26:23 +02:00
  • 03a2c8ef7c Finished restructuring the OBIDMS_column class properties Celine Mercier 2016-09-27 14:16:30 +02:00
  • a7f891d1c9 Added a lines_used property to the OBIDS_column class Celine Mercier 2016-09-26 18:04:28 +02:00
  • bd50b3f972 Added version property to OBIDMS_column class Celine Mercier 2016-09-26 17:45:10 +02:00
  • 81380363b7 Added original_name property to OBIDMS_column class Celine Mercier 2016-09-26 17:31:32 +02:00
  • a4b8349274 Added data_type property to OBIDMS_column class Celine Mercier 2016-09-26 17:12:20 +02:00
  • a474391b27 Added nb_elements_per_line property to OBIDMS_column class Celine Mercier 2016-09-26 17:01:13 +02:00
  • a0bc45cc92 Added elements_names property to OBIDMS_column class Celine Mercier 2016-09-26 16:53:16 +02:00
  • 76f89717fe Added alias property to OBIDMS_column cython class Celine Mercier 2016-09-26 16:12:48 +02:00
  • b408a4f6eb Changed file name limits to adapt to system limits + minor changes Celine Mercier 2016-09-22 18:05:07 +02:00
  • b083745f56 Deleted the "new line selection while editing a view" system Celine Mercier 2016-09-22 11:19:29 +02:00
  • 43f3c69a40 Fixed bug when cloning column with line selection Celine Mercier 2016-09-21 17:50:21 +02:00
  • e79507b629 Fixed bugs in the process ensuring that all the columns of a view have the same line count, fixed a bug when trying to set a value in a view when a line selection exists, fixed a bug when adding a new column to a view where line counts would be wrong Celine Mercier 2016-09-21 17:42:17 +02:00
  • bb25723d99 Improved documentation of a function Celine Mercier 2016-09-21 17:30:39 +02:00
  • a0da984003 Fixed bug where columns would not get truncated to the right size, and fixed bug where column directories would be open and not closed in some instances Celine Mercier 2016-09-21 17:28:52 +02:00
  • 802bae110b Removed deprecated function Celine Mercier 2016-09-21 17:09:59 +02:00
  • dd55aef3e5 Added column class method to get the unique references (name and version) of a column Celine Mercier 2016-09-21 17:08:44 +02:00
  • 9ac522fde1 Better obi test command Celine Mercier 2016-09-21 17:06:35 +02:00
  • 6adb9eb623 Should solde issue #56 coissac 2016-09-19 21:40:40 +02:00
  • 8f49553d5a First version of the obi test command, testing that the OBITools3 work correctly Celine Mercier 2016-09-15 12:26:07 +02:00
  • 986f90c59e Fixed bug where column directories weren't closed correctly, leading to too many file descriptors open, and added error checking when closing file descriptors Celine Mercier 2016-09-15 12:18:40 +02:00
  • a240ec0169 Added error checking when closing file descriptors Celine Mercier 2016-09-15 11:58:56 +02:00
  • 0a3c23d9d0 Added a missing closedir Celine Mercier 2016-09-15 11:58:34 +02:00
  • 8724445fa1 Added error checking when closing files Celine Mercier 2016-09-15 11:50:30 +02:00
  • de189fd7e0 Fixed major bug when cloning an AVL where the bloom filter was not copied properly (because the sutructure copy via assignation does not work for structures with a variable size) Celine Mercier 2016-09-15 11:47:02 +02:00
  • 9a97f1f633 View predicates are now carried over when cloning a view Celine Mercier 2016-09-06 16:22:24 +02:00
  • 00014eb023 View files now have the *.obiview extension Celine Mercier 2016-09-06 14:19:13 +02:00
  • acc0da2d0b Readjusted some limits for file names and file numbers to be under OS limits Celine Mercier 2016-09-05 12:39:04 +02:00
  • 668696fc5a Fixed major bug: when setting all the columns of a view to the same number of lines, columns are now cloned before being enlarged if needed + predicate functions now print error messages if the predicates are not respected Celine Mercier 2016-09-05 12:37:36 +02:00
  • ba84ef4847 Fixed typo Celine Mercier 2016-09-05 12:31:06 +02:00
  • c9dce03295 Fixed major bug when cloning an AVL group (last AVL of new group was not correctly enlarged before copying the data) + minor improvements Celine Mercier 2016-09-05 12:29:52 +02:00
  • eb82d088cb Added some view class methods Celine Mercier 2016-09-05 12:20:00 +02:00
  • f46ea0b988 Finished fixing issues with DMS paths Celine Mercier 2016-08-30 11:09:45 +02:00
  • 5b2e370ffb Fixed a bug when using an absolute path for a DMS Celine Mercier 2016-08-29 17:30:31 +02:00
  • 8d360b0fac Minor improvements to obi export command Celine Mercier 2016-08-19 17:49:22 +02:00
  • b34769b27c Minor improvements to obi export command Celine Mercier 2016-08-19 17:46:55 +02:00
  • 2d0a714e37 Basic obi export command exporting from view to fasta or fastq format, for testing purposes Celine Mercier 2016-08-19 17:40:58 +02:00
  • 7b780ffb28 View files now have a dynamic size to allow unlimited comments size Celine Mercier 2016-08-18 17:57:03 +02:00
  • e4129610cf Quality columns are now optional in NUC_SEQS views + minor fixes Celine Mercier 2016-08-16 15:17:26 +02:00
  • cf839522e7 Minor update and fix to obi grep command Celine Mercier 2016-08-12 17:45:44 +02:00
  • 10b22f79da The cython subclass is now correctly chosen when cloning a view Celine Mercier 2016-08-12 17:39:19 +02:00
  • ad8e10f2d1 Reworked a bit alignment API Celine Mercier 2016-08-12 15:56:07 +02:00
  • 92cad61417 Fixed bug when closing views with no associated predicate Celine Mercier 2016-08-12 15:52:38 +02:00
  • 64a745ce0b First very basic version of obi grep command Celine Mercier 2016-08-11 17:32:08 +02:00
  • 2d8ac2b035 Fixed bug when creating an OBI_IDX column Celine Mercier 2016-08-11 17:30:32 +02:00
  • 5b7917bb5a Fixed bug when writing predicates in view file Celine Mercier 2016-08-11 17:30:09 +02:00
  • d3c58780a0 Added __len__ function do OBIViews that returns the line count Celine Mercier 2016-08-10 17:20:23 +02:00
  • 029d395da1 Added __iter__ function to OBIView lines Celine Mercier 2016-08-10 17:08:22 +02:00
  • bea02cc7a5 Added (temporary?) check for the type of quality strings because the import now seems to return them with bytes type Celine Mercier 2016-08-10 16:25:45 +02:00
  • 4ba01617af Fixed obscure compilation bug Celine Mercier 2016-08-10 15:26:40 +02:00
  • bec684d5e2 Fixed merge conflict Celine Mercier 2016-08-10 15:05:37 +02:00
  • 2aaa87edcc 1st version of obi align command and reworked functions that handle column alignment Celine Mercier 2016-08-10 14:51:02 +02:00
  • 400a3f9f3d Merge branch 'Eric_version_for_sequence' coissac 2016-08-04 09:42:42 +02:00
  • d1d26b9028 Simplify the code Eric_version_for_sequence coissac 2016-08-04 08:00:54 +02:00
  • 465ea81c77 Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git coissac 2016-08-03 10:13:47 +02:00
  • 1e6d6e32e0 Switch to Cython version >= 0.24 coissac 2016-08-03 10:13:10 +02:00
  • ccc877764e Patch a bug in the printing of the progress bar leading to a bus error when compiled with some C compilers and Cython >= 0.24 coissac 2016-08-03 10:12:23 +02:00
  • 8f0462c407 Merge branch 'master' into Eric_version_for_sequence coissac 2016-08-03 10:09:20 +02:00
  • 26b8e1f215 Modified C API to set and get in columns: added functions to set and get using column names instead of pointers, and changed function names Celine Mercier 2016-08-02 16:33:19 +02:00
  • 312f50ff0f Major update: Column aliases. Columns are now identified in the context of a view by an alias that can be modified. Celine Mercier 2016-08-01 18:25:30 +02:00
  • 3843485a04 Deleted deprecated function declaration that would make compilation impossible and fixed error in documentation Celine Mercier 2016-07-22 16:21:02 +02:00
  • 20425a5d2b Deleted deprecated structure declarations Celine Mercier 2016-07-19 15:48:56 +02:00
  • 56e4848ebd The predicates associated with a view are now described in its comments field Celine Mercier 2016-07-19 15:31:21 +02:00
  • 8850e40b6e Minor changes for better presentation Celine Mercier 2016-07-19 15:30:17 +02:00
  • b89af38109 Goes with 38718320 Celine Mercier 2016-07-18 13:57:49 +02:00
  • 38718320f9 First version for the association of one column to another. Closes #55 Celine Mercier 2016-07-15 15:38:49 +02:00
  • 8ee85c3005 A first version of predicate functions that are checked when a new view is saved and closed Celine Mercier 2016-07-12 14:54:11 +02:00
  • 000b9999ad Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git coissac 2016-07-03 09:22:22 +02:00
  • aff9831c13 Substitute fprintf call by fputs call to conform with the new ubuntu compilation rules coissac 2016-07-03 09:21:56 +02:00
  • 448fa8d325 first trial for a fasta formater coissac 2016-07-03 09:18:52 +02:00
  • 6af62d8124 Change a fprintf without argument to a fputs to comply with the new default parameter on ubuntu coissac 2016-07-03 08:25:06 +02:00
  • 0869b9ba3f Closes issue #47 by storing each view in a separate file named with the view's name and created upon view creation. Celine Mercier 2016-06-30 11:41:30 +02:00
  • ad2af0b512 Some comments updated Celine Mercier 2016-06-16 11:26:54 +02:00
  • 38e603ed57 Deleted some redundant cython code Celine Mercier 2016-06-10 10:34:47 +02:00
  • f438c3d913 OBIQUAL columns can now handle multiple elements per line Celine Mercier 2016-06-09 15:54:36 +02:00
  • 2a1ea3ba3f Setting NA values is now handled properly for OBI_SEQ, OBI_STR and OBI_QUAL columns Celine Mercier 2016-06-09 14:22:36 +02:00
  • fc3641d7ff Read-only AVLs are now hard-linked instead of copied when cloning an AVL group to make it writable. Also fixed several bugs when handling AVL groups. Celine Mercier 2016-06-03 19:02:46 +02:00
  • 799b942017 Deleted old debugging print Celine Mercier 2016-06-03 18:57:32 +02:00
  • 6e3f5b230e Fixed typo in doc Celine Mercier 2016-06-03 18:56:45 +02:00
  • 2f57f80c63 Fixed a bug where an unmapped variable would be read Celine Mercier 2016-06-03 18:55:58 +02:00
  • 2962c4d250 Goes with previous commit Celine Mercier 2016-06-03 18:54:25 +02:00
  • 69bf7ec2e7 NA value for OBI_STR and OBI_SEQ columns is now NULL Celine Mercier 2016-06-03 18:53:22 +02:00
  • bac7ce7184 Start of the implementation of the export methods coissac 2016-06-02 19:10:33 +02:00
  • f186395661 Trap potential exception generated by char* to bytes casts coissac 2016-05-29 21:18:20 +02:00
  • 85395dfc1a value returned for sequence is now bytes and no more str coissac 2016-05-29 13:53:32 +02:00
  • f830389974 Add some comment on the location of the align method. coissac 2016-05-29 12:58:31 +02:00
  • 2e35229357 Add conversion checking on the value of a seq column coissac 2016-05-29 12:54:13 +02:00
  • a8ed57dc6e few small changes coissac 2016-05-21 12:29:55 +02:00
  • c3274d419c remove an extra debug log coissac 2016-05-21 12:29:08 +02:00
  • cca0dbb46b Close issue #54 by adding a read1 method to the MagicKeyFile class coissac 2016-05-21 12:24:48 +02:00