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  • 019dfc01b4 Branch to refactor and debug (AVLs bugged) Celine Mercier 2016-04-08 15:38:57 +02:00
  • 45c9c5075c A first version of the fasta parser Eric Coissac 2016-04-01 18:15:54 +02:00
  • 20b97c972b Add boolean type in the tag evaluation Eric Coissac 2016-04-01 13:42:24 +02:00
  • efc4a4a3c6 Reduce the call count to eval. This reduce by 3 the time of fast(q|a) header processing Eric Coissac 2016-04-01 08:54:06 +02:00
  • ce6ea89c21 Add the missing bootstrappip module Eric Coissac 2016-03-31 17:28:03 +02:00
  • 4207db7c17 Transfers bug patch from orgasm Eric Coissac 2016-03-31 16:53:09 +02:00
  • 1cd35b3359 firt version of a fastq parser Eric Coissac 2016-03-31 10:47:12 +02:00
  • f51a6df5b2 Add a class buffering lines during a text file reading Eric Coissac 2016-03-30 14:53:25 +02:00
  • 94417e1330 patch the uncompress module to be able to deal with remote file Eric Coissac 2016-03-29 20:57:39 +02:00
  • 2e17dbce55 Adds a uopen function able to open transparently a local or a remote file compressed or not Eric Coissac 2016-03-29 20:56:54 +02:00
  • a9eed1f5d9 Adds class for uncompressing transparently compressed files on line Eric Coissac 2016-03-29 18:21:04 +02:00
  • 2dfab3f378 Some changes in relation with the new obitools3.apps module Eric Coissac 2016-03-28 15:05:59 +02:00
  • e583098a96 change in the obi programme according to the new obitools3.apps module creation Eric Coissac 2016-03-28 15:05:02 +02:00
  • b926ca3997 A template for a command Eric Coissac 2016-03-28 15:04:06 +02:00
  • aacfefad26 A set of utilitaty function for creating commands Eric Coissac 2016-03-28 15:03:26 +02:00
  • edc4fd7b3e Fixed minor warning Celine Mercier 2016-03-25 16:11:52 +01:00
  • ff6c27acf2 Implemented the retrieval of values with groups of AVLs check_avl_data_with_crc Celine Mercier 2016-03-25 15:35:16 +01:00
  • 69856f18dd untested (and no possible retrieval) of CRC used to represent data in AVL trees Celine Mercier 2016-03-24 16:38:11 +01:00
  • 2c084c8cf7 Switch to 10000000 per avl Eric Coissac 2016-03-23 16:13:28 +01:00
  • 58ac860cc7 Added macro for the bloom filter parameters and deleted old unused macros for crc Celine Mercier 2016-03-23 13:33:40 +01:00
  • d44117d625 obiimport function for testing purposes Celine Mercier 2016-03-23 13:00:02 +01:00
  • 6bd42132c4 Minor fixes to silence warnings and replaced two asprintf uses Celine Mercier 2016-03-23 12:58:53 +01:00
  • 4085904362 Merge branch 'multiple_avls_bloom' Celine Mercier 2016-03-22 14:14:10 +01:00
  • b04b4b5902 made POSIX compliant Celine Mercier 2016-03-21 11:33:06 +01:00
  • 383e738ab7 Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git Celine Mercier 2016-03-18 15:49:53 +01:00
  • 3681cecb4d Multiple AVLs with bloom filters (very raw test version) multiple_avls_bloom Celine Mercier 2016-03-18 11:06:02 +01:00
  • eaf5fd940a remap every 100000 values always_remap_AVL Celine Mercier 2016-03-14 17:03:24 +01:00
  • 545ed8111a Code for tests storing data in multiple AVLs. (note: unretrievable data as implemented) multiple_avls Celine Mercier 2016-03-11 15:34:55 +01:00
  • 86071d30c9 Minor improvement in AVL initial size calculation NoSQL Celine Mercier 2016-03-11 14:07:40 +01:00
  • 21d1b2ed3e First implementation of taxonomy reading Celine Mercier 2016-03-11 13:56:38 +01:00
  • 6157633137 prototype for the obi unix command and the count sub command Eric Coissac 2016-03-08 16:06:00 +01:00
  • a08def47e6 It is now impossible to create a view with a name identical to one of an existing written view Celine Mercier 2016-03-01 13:36:54 +01:00
  • fc5a12bad7 Closes #34 Celine Mercier 2016-02-29 17:56:55 +01:00
  • e323d8e702 Cython classes for nucleotide sequences (outside or in the context of a view) Celine Mercier 2016-02-29 16:33:30 +01:00
  • b350ea0393 Fixed minor error Celine Mercier 2016-02-29 16:28:34 +01:00
  • 8e9e21a02e Increased the maximum depth of AVL trees Celine Mercier 2016-02-29 16:27:23 +01:00
  • 4df313c54a Added Obiviews specialized for the handling of nucleotide sequences Celine Mercier 2016-02-25 09:43:27 +01:00
  • ffc68d448f Deleted a forgotten print statement Celine Mercier 2016-02-18 15:15:42 +01:00
  • a8f03248a8 Major update : views Celine Mercier 2016-02-18 10:38:51 +01:00
  • cfaf069095 Fixed more typos and formatting imperfections. Celine Mercier 2015-12-11 17:37:25 +01:00
  • a6144eabe2 Fixed typos Celine Mercier 2015-12-11 17:26:20 +01:00
  • c139367555 DNA sequences and character strings are now handled using AVL trees. Celine Mercier 2015-12-11 17:24:44 +01:00
  • 1586956d57 Added the lists of opened columns and arrays in the OBIDMS structure, and a counter in the OBIDMS column structure; fixed some bugs and created tests for referring columns that are bound to disappear anyway. Celine Mercier 2015-12-02 17:32:07 +01:00
  • b45b496b0e Major update: new type of columns containing indices referring to lines in other columns Celine Mercier 2015-11-29 11:57:07 +01:00
  • 2cf10cb6f0 Column type is now passed as a character string when creating the column (either 'OBI_INT', 'OBI_FLOAT', 'OBI_BOOL', 'OBI_CHAR', 'OBI_STR' or 'OBI_SEQ') Celine Mercier 2015-11-23 15:48:27 +01:00
  • 5a5516303d deleting useless .pyc files Celine Mercier 2015-11-23 14:43:34 +01:00
  • d6a99bafea Fixed a major bug with the versioning of columns that was introduced in f6ec8ba9 Celine Mercier 2015-11-23 13:34:51 +01:00
  • 08f2657e18 Increased maximum line count of columns to 1^9 Celine Mercier 2015-11-23 13:23:18 +01:00
  • 6aa2f92930 DNA sequences are now encoded on 4 bits when they are in IUPAC Celine Mercier 2015-11-20 15:32:09 +01:00
  • 87044b41d8 modified the encoding function on 2 bits a little Celine Mercier 2015-11-20 11:32:47 +01:00
  • 6ab1c83302 New column type for DNA sequences. Only for those coded on 2 bits (only 'ATGCatgc') for now. Celine Mercier 2015-11-19 18:12:48 +01:00
  • e371248567 changed version to 0.0.0 Celine Mercier 2015-11-19 18:11:21 +01:00
  • dbf9463238 The endianness of a DMS is now stored in the OBIDMS structure Celine Mercier 2015-11-18 15:35:09 +01:00
  • eb12af4da4 Fixed minor error in the documentation of a function. Celine Mercier 2015-11-16 15:38:01 +01:00
  • e8417b4f6f The endianness of an OBIDMS is now stored in an informations file that is read when opening the OBIDMS. Celine Mercier 2015-11-16 14:37:51 +01:00
  • 6579566c6e Minor changes in code to improve readability and fix C compilation warnings Celine Mercier 2015-11-10 14:37:58 +01:00
  • 410e2e02a0 When retrieving the header of a column, the version number of the column wanted can now be provided. Celine Mercier 2015-11-10 13:30:10 +01:00
  • 8ce4f264aa When enlarging a column, the function doesn't try anymore to keep the mapped region at the same pointer (never works), and unmap/remap instead. Celine Mercier 2015-11-10 13:18:36 +01:00
  • d885eb48ff The header size when creating a column is now calculated according to the size of the header structure and the page size of the platform. Celine Mercier 2015-11-10 13:09:30 +01:00
  • 661fe3606a In OBI_CHAR columns, characters are now given and retrieved as decoded (unicode) characters. Celine Mercier 2015-11-10 11:24:08 +01:00
  • c4b7e579cf Comments in column headers are now working. Celine Mercier 2015-11-10 10:56:45 +01:00
  • f6ec8ba963 The header size is now directly read in the file when a column or an array is opened. Celine Mercier 2015-11-09 17:50:32 +01:00
  • 0e3d6ed2d7 Methods __len__ (number of lines used) and __sizeof__ (total size in bytes) implemented for columns. Celine Mercier 2015-11-09 15:56:20 +01:00
  • 01bfc14503 The data size in bytes is now stored in the header of a column. Celine Mercier 2015-11-09 15:55:00 +01:00
  • 65c1b1e8b2 Minor changes to make the creation of files and directories cleaner Celine Mercier 2015-11-09 15:22:01 +01:00
  • b37bd8f21c File descriptors for dms, column and array directories are now stored in structures. Celine Mercier 2015-11-09 15:06:02 +01:00
  • 05e3956a0c Minor changes in code to improve readability (freeing some character strings earlier) Celine Mercier 2015-11-09 11:22:51 +01:00
  • 9b066f4327 Major update: obiarrays with columns containing indices referring to character strings. cython_bug Celine Mercier 2015-11-06 17:55:15 +01:00
  • 456551ffeb obi arrays that don't work because of cython bug passing wrong pointers Celine Mercier 2015-11-03 14:22:00 +01:00
  • ecb9d97adb Reorganized the code to have less functions, and the functions to get and format the creation date of a column are now working. Celine Mercier 2015-10-15 15:12:45 +02:00
  • 0eaa5aa784 Major changes : new cython subclasses to handle columns with multiple elements per line in a more efficient way + now elements_names are passed as a list + new function to recover only the header of a column Celine Mercier 2015-10-14 18:05:34 +02:00
  • 21923e213d The unit tests now test for None values Celine Mercier 2015-10-12 18:02:40 +02:00
  • 6877fc4892 Fixed a critical bug where values were initialized to NA at the wrong location when there was multiple elements per line Celine Mercier 2015-10-12 17:54:36 +02:00
  • dbed3d9d1d New module for unit testing with PyUnit Celine Mercier 2015-10-09 15:42:57 +02:00
  • fc8bf16769 Fixed a critical bug in the computation of the new number of lines of a column when truncating Celine Mercier 2015-10-09 13:49:48 +02:00
  • e114a3c9cb fixed a critical bug where data size was not calculated correctly and column directory is now closed when column is closed Celine Mercier 2015-10-09 10:25:40 +02:00
  • ebc9f6f512 fixed a bug where Cython was casting doubles in floats Celine Mercier 2015-10-08 15:28:30 +02:00
  • 2b3f03ec28 Removed deprecated script Celine Mercier 2015-10-08 10:46:46 +02:00
  • 8fd9c06be2 Fixed missing file for documentation compilation Celine Mercier 2015-10-08 10:45:54 +02:00
  • b553eef781 Method to close a DMS is uncommented but not complete yet (columns have to be closed separately) Celine Mercier 2015-10-08 10:44:13 +02:00
  • ee4c513fd4 Fixed a bug where cloning a column would fail if the data was empty Celine Mercier 2015-10-08 10:36:02 +02:00
  • c013e6ad33 fixed typo in doxygen doc Celine Mercier 2015-10-08 10:33:19 +02:00
  • c98d567e2f Updated the documentation and restructured a bit because it wasn't compiling (note: Breathe not working) Celine Mercier 2015-10-06 11:09:01 +02:00
  • 392f110c8d new functions in the OBIDMS_column class to raise NotImplementedError exceptions and to get the creation date of a column Celine Mercier 2015-10-02 13:51:26 +02:00
  • 6ced3c4896 new functions to get the creation date of a column Celine Mercier 2015-10-02 13:47:53 +02:00
  • 4b8bf41a71 closes #13, obi_errno is initialized to 0 Celine Mercier 2015-10-02 13:46:34 +02:00
  • c59a244e9d Fixed little typo Celine Mercier 2015-09-30 12:07:13 +02:00
  • 4b7f2d268b Doxygen documentation corrected and completed. Celine Mercier 2015-09-30 12:03:46 +02:00
  • 45af8396b8 minor change in variable name for better coherence cython_things Celine Mercier 2015-09-28 13:52:41 +02:00
  • eeebbc77c3 missing __init__ file in previous commit Celine Mercier 2015-09-28 13:52:13 +02:00
  • 72155c3b73 entirely reworked cython wrapper Celine Mercier 2015-09-28 13:51:35 +02:00
  • 9aaf2d264a test Celine Mercier 2015-09-25 11:29:17 +02:00
  • 0951934f77 test Celine Mercier 2015-09-25 11:28:23 +02:00
  • 68b6ab3224 working on the cython wrapper. This doesn't compile Celine Mercier 2015-09-24 11:32:09 +02:00
  • b0570ee486 fixed permissions when creating files Celine Mercier 2015-09-22 15:52:07 +02:00
  • 72105b2aed fixed the computation of the data size when cloning a column Celine Mercier 2015-09-22 10:27:17 +02:00
  • 9ab8a42340 fixed the mkdir permission mode that forced the user to use sudo to write in the created directories Celine Mercier 2015-09-21 15:48:02 +02:00
  • 7b606c0477 Column files now always have a size that is a multiple of the page size, and the function that enlarges mapped column files tries mapping on next byte before unmapping/mapping again Celine Mercier 2015-09-21 15:42:29 +02:00
  • 7d7dbb1bf9 Handling of single char columns Celine Mercier 2015-09-18 15:49:15 +02:00
  • 34a3717fb9 The cython function to open a column is now a method of the OBIDMS class Celine Mercier 2015-09-17 11:23:50 +02:00