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  • 5a78157112 increase parsing speed of the header Eric Coissac 2016-05-21 10:29:11 +02:00
  • 0b9a41d952 Patch a bug about the reading of the last sequence Eric Coissac 2016-05-21 10:28:03 +02:00
  • e681ca646d Fixed a problem with some columns being shorter in views and triggering errors when trying to get values. Temporary fix that needs discussion Celine Mercier 2016-05-20 18:45:29 +02:00
  • 3b59043ea8 Major update: New column type to store sequence qualities. Closes #41 Celine Mercier 2016-05-20 16:45:22 +02:00
  • ffff91e76c Fixed variable name that had been accidentally changed for better clarity Celine Mercier 2016-05-18 13:27:41 +02:00
  • 6a8df069ad Indexers are now cloned if needed to modify them after they've been closed. Obligatory indexers' names now follow the same pattern as other indexers (columnname_version). Closes #46 and #49. Celine Mercier 2016-05-18 13:23:48 +02:00
  • 8ae7644945 First version of quality handling (not working yet) and now it is checked that a column is writable before enlarging it Celine Mercier 2016-05-11 16:38:14 +02:00
  • b3c47809da First version of alignment functions (imported from suma* programs) Celine Mercier 2016-05-11 16:36:23 +02:00
  • 3567681339 Now when a column is added to a view, if there is a line selection, all columns in the view are cloned first Celine Mercier 2016-05-11 16:34:20 +02:00
  • 757ef8509a Deleting CeCILL license duplicates Celine Mercier 2016-05-09 11:17:45 +02:00
  • f961621f5d Minor improvements in _obidms Cython layer Celine Mercier 2016-05-04 13:43:26 +02:00
  • 1a2d552567 Abandoned beginning of functions to apply comparisons to whole columns (not worth it for now as comparisons are already fast enough) abandoned_branch_for_column_comparison_functions Celine Mercier 2016-05-04 13:39:55 +02:00
  • bc12360490 Reworked and commented a bit the cython layer for dms, columns and views Celine Mercier 2016-05-02 15:16:06 +02:00
  • 872071b104 Removed a list of column pointers kept in the OBIView class that was not really needed Celine Mercier 2016-05-02 14:23:42 +02:00
  • 32cc8968e8 Adding CeCILL license Celine Mercier 2016-05-02 11:51:59 +02:00
  • d6481f0db8 Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git Celine Mercier 2016-04-29 17:46:59 +02:00
  • a32920e401 Relative paths when creating or opening a DMS now work Celine Mercier 2016-04-29 17:46:36 +02:00
  • 31cf27d676 Added indexer function that returns the name of the indexer Celine Mercier 2016-04-29 16:18:56 +02:00
  • baba2d742e commenting _obidms.pyx Celine Mercier 2016-04-29 16:07:03 +02:00
  • 5bd12079ae Added comments about listing columns and indexers in obidms functions Celine Mercier 2016-04-29 16:06:01 +02:00
  • 072ee5ac03 Re-re-fixed line breaks in README file Celine Mercier 2016-04-29 15:44:40 +02:00
  • 9fe21316ff Refixed line breaks in README file Celine Mercier 2016-04-29 15:39:46 +02:00
  • 3dc3aaa46b Fixed line breaks in README file Celine Mercier 2016-04-29 15:36:58 +02:00
  • b371030edd Adding README file Celine Mercier 2016-04-29 15:35:08 +02:00
  • b3976fa461 Merge branch 'luke_tests' Celine Mercier 2016-04-28 11:17:24 +02:00
  • 6ea2cfb9ca Merging luke_tests branch without the commit turning inline functions in macros Celine Mercier 2016-04-28 11:17:18 +02:00
  • 0eca86107e Pseudo obihead for tests luke_tests Celine Mercier 2016-04-27 14:27:28 +02:00
  • 0de953a3ef pseudo obigrep for tests Celine Mercier 2016-04-27 14:19:55 +02:00
  • f3b20b809d Fixed bug with indexer names being defined and generating seg fault if creating a column not using indexers Celine Mercier 2016-04-27 14:01:36 +02:00
  • d159b921eb Fixed obi import trying to print all lines at the end (source of segfault?) Celine Mercier 2016-04-27 13:14:19 +02:00
  • 4e4cf46b16 Added all C files as source files for all cython files to stop having that kind of problem with linux systems Celine Mercier 2016-04-27 10:44:24 +02:00
  • 6b61533650 Added more C source files for _obiseq Celine Mercier 2016-04-27 10:41:00 +02:00
  • 419885485b Added files in _obitaxo C sources for cython Celine Mercier 2016-04-27 10:30:16 +02:00
  • 0c8504b6db Commented #ifdef directive for detect_bucket_size function because it causes errors Celine Mercier 2016-04-27 10:24:40 +02:00
  • 654c34a1a6 changed inline functions to macros to make it work on Luke Celine Mercier celine.mercier@ujf-grenoble.fr 2016-04-26 15:40:12 +02:00
  • 2d8c06f7b7 Fixed variable initialization for error detection Celine Mercier 2016-04-26 14:38:46 +02:00
  • a6c8d35491 import command a bit modified for tests Celine Mercier 2016-04-26 14:29:54 +02:00
  • 366264828e Renamed MurmurHash2.c file to murmurhash2.c as it could be a problem Celine Mercier 2016-04-26 14:29:17 +02:00
  • d3a6ff6043 Removed deprecated code Celine Mercier 2016-04-26 14:27:16 +02:00
  • 5ca84b91dc Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git Celine Mercier 2016-04-25 18:35:57 +02:00
  • 87935c6678 Fixed all compilation problems with new function names, locations etc Celine Mercier 2016-04-25 18:35:02 +02:00
  • 92980508c0 Made the function to clone a column in the context of a view private Celine Mercier 2016-04-25 18:15:25 +02:00
  • 65880db422 Made function to update the line count of a view private Celine Mercier 2016-04-25 18:11:37 +02:00
  • 767d9c7804 Reordered view functions for better coherence Celine Mercier 2016-04-25 18:07:58 +02:00
  • 2566377e2a Updated the documentation for utils functions Celine Mercier 2016-04-25 18:02:58 +02:00
  • 1fbbdd43f9 Updated obiversion_t declaration Celine Mercier 2016-04-25 17:58:37 +02:00
  • 8cdfbb379e Documentation for views and reworked the code a little Celine Mercier 2016-04-25 17:58:12 +02:00
  • 0a55e26520 Reworked obiview code and added more comments Celine Mercier 2016-04-25 11:37:53 +02:00
  • 68a8509c12 Updated documentation in obitypes.h Celine Mercier 2016-04-25 10:33:01 +02:00
  • 5f98d2ed5c Fixed the calculation of the size of data for OBI_STR and OBI_SEQ columns Celine Mercier 2016-04-25 10:26:51 +02:00
  • ef1be141c1 Update Licence to english version Eric Coissac 2016-04-23 18:03:50 +02:00
  • bbfd40d56d Add license Eric Coissac 2016-04-23 18:03:10 +02:00
  • 5d08da46a2 Updated the documentation in obidmscolumn.h Celine Mercier 2016-04-22 17:55:53 +02:00
  • 66045acf1d Creating a column now uses the function to create the indexer name if one was not provided Celine Mercier 2016-04-22 17:47:00 +02:00
  • 6977c4315c Improved function to build an indexer name Celine Mercier 2016-04-22 17:38:23 +02:00
  • 839b3000a8 Added a function to build indexer names Celine Mercier 2016-04-22 17:08:23 +02:00
  • ffa4557928 changed MAP_PRIVATE flags to MAP_SHARED when opening a column because it seems a lot more efficient Celine Mercier 2016-04-22 16:26:24 +02:00
  • 003cd11362 Fixed initialization of NA values for OBI_STR and OBI_SEQ columns Celine Mercier 2016-04-22 16:14:23 +02:00
  • c87227b65a Uncommented an error message that doesn't need to be commented anymore Celine Mercier 2016-04-22 16:11:56 +02:00
  • c07e75f2ac Updated the documentation for OBI_STR columns Celine Mercier 2016-04-22 15:59:32 +02:00
  • 6b394a5cf7 Updated the documentation for OBI_SEQ columns Celine Mercier 2016-04-22 15:58:20 +02:00
  • 2416b8ccd8 Deleted more unused inclusions in OBI_STR and OBI_SEQ column types code Celine Mercier 2016-04-22 15:56:09 +02:00
  • b9921e111d Removed unused inclusions and definitions in all column types code Celine Mercier 2016-04-22 15:50:19 +02:00
  • 8f5aa8841d Removed unused definition in OBI_IDX columns code Celine Mercier 2016-04-22 15:44:30 +02:00
  • 900d67de87 Updated the documentation for columns with the type OBI_IDX Celine Mercier 2016-04-22 15:43:39 +02:00
  • 22e3c3eeed Updated the documentation for obidms functions Celine Mercier 2016-04-22 11:28:09 +02:00
  • 4ead37ee48 Finished moving obiblob functions to obiblob files and documentation for obiblob functions Celine Mercier 2016-04-21 15:18:14 +02:00
  • bce360bbd5 Documentation for obiblob indexer API Celine Mercier 2016-04-21 15:08:40 +02:00
  • 2a68cb26f8 Improved AVL tree documentation Celine Mercier 2016-04-21 15:07:27 +02:00
  • 043e70ff49 Updated AVL documentation Celine Mercier 2016-04-21 14:39:03 +02:00
  • 66021367f6 Moved some blob functions to obiblob.c Celine Mercier 2016-04-21 14:20:26 +02:00
  • e69f44ae3d Little annotations for the murmur hash function. Celine Mercier 2016-04-21 13:53:29 +02:00
  • 1941a3785e Updated encode functions documentation Celine Mercier 2016-04-21 13:46:02 +02:00
  • c7b8db6a2e Replaced malloc+memset with calloc Celine Mercier 2016-04-21 13:45:39 +02:00
  • 1dc4a3be49 Documentation for DNA sequence indexing functions Celine Mercier 2016-04-21 13:36:51 +02:00
  • 09597016fd Short doc for crc function Celine Mercier 2016-04-21 13:23:52 +02:00
  • 1a2fa0923c Documented the functions indexing and retrieving character strings Celine Mercier 2016-04-21 11:35:21 +02:00
  • 00f2f2cc51 Documented changes made in bloom functions Celine Mercier 2016-04-21 11:22:31 +02:00
  • 7a88ca619a First obi import (doesn't import tags yet because NA values aren't handled) Celine Mercier 2016-04-15 17:00:08 +02:00
  • eddd19a245 Changes in obi commands Celine Mercier 2016-04-15 16:59:21 +02:00
  • 2aafecc3b5 Changed sequence 'description' to 'definition' everywhere Celine Mercier 2016-04-15 16:31:43 +02:00
  • 094b2371e9 Deleted obsolete directory Celine Mercier 2016-04-15 14:44:31 +02:00
  • c1034d300d merging and fixed git conflict with obiavl.h Celine Mercier 2016-04-15 13:23:29 +02:00
  • 02d67c257f The default name of an AVL is now the column name + '_indexer', and when an AVL is opened (as opposed to created), it is read-only refactoring_debugging Celine Mercier 2016-04-15 12:55:26 +02:00
  • e04ea85d1e Fixed problematic __str__ method and useless declarations in the OBI_Nuc_Seq_Stored class Celine Mercier 2016-04-15 11:22:05 +02:00
  • 527d3555f0 Moved the functions getting full paths for files and directories to obidms.c/.h files Celine Mercier 2016-04-15 11:11:13 +02:00
  • 71492ad229 Made the handling of listing and unlisting opened columns and indexers functions in the obidms files. Celine Mercier 2016-04-15 10:49:12 +02:00
  • 73d64e5aff Renamed 'unmap_header' function to 'close_header' Celine Mercier 2016-04-14 15:19:27 +02:00
  • 4cb52e1632 Made the truncating of columns automatic when closing them (note: already the case for AVLs) Celine Mercier 2016-04-14 15:13:30 +02:00
  • 9d042f7bd0 Refactored and relocated the set and get functions of all column types, both within and out of the context of a view Celine Mercier 2016-04-13 15:10:24 +02:00
  • 5ec2d8842e Character string indexer API Celine Mercier 2016-04-12 17:21:01 +02:00
  • 04c9470f7d Fixed and cleaned DNA_seq_indexer API Celine Mercier 2016-04-12 17:20:24 +02:00
  • be05c889e2 DNA_seq_indexer API Celine Mercier 2016-04-12 16:38:47 +02:00
  • 04e3a7b5a9 Added more references in cython .cfiles files because it seems necessary for linux distributions Celine Mercier 2016-04-12 15:10:54 +02:00
  • d8107533d8 Obiblob_indexer API Celine Mercier 2016-04-12 14:53:33 +02:00
  • cd4e65e190 Fixed typo and includes in obiblob files Celine Mercier 2016-04-12 14:52:27 +02:00
  • 375bfcce8a Renamed "Obi_byte_arrays" to "Obiblobs" and moved Obiblob functions to separate obiblob.c and obiblob.h files Celine Mercier 2016-04-12 11:21:14 +02:00
  • c225cfd8b6 Fixed bug with retrieval of values from AVLs (bad cast in byte array structure) Celine Mercier 2016-04-11 17:07:22 +02:00
  • 6fe4c6134a Allows for calling getConfiguration without parametter for geting the default configuration Eric Coissac 2016-04-11 13:31:09 +02:00
  • 966b1325ed Deleted declaration of obsolete public function Celine Mercier 2016-04-11 11:14:20 +02:00