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1cd35b3359
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firt version of a fastq parser
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2016-03-31 10:47:12 +02:00 |
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f51a6df5b2
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Add a class buffering lines during a text file reading
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2016-03-30 14:53:25 +02:00 |
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94417e1330
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patch the uncompress module to be able to deal with remote file
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2016-03-29 20:57:39 +02:00 |
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2e17dbce55
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Adds a uopen function able to open transparently a local or a remote
file compressed or not
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2016-03-29 20:56:54 +02:00 |
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a9eed1f5d9
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Adds class for uncompressing transparently compressed files on line
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2016-03-29 18:21:04 +02:00 |
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2dfab3f378
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Some changes in relation with the new obitools3.apps module
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2016-03-28 15:05:59 +02:00 |
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e583098a96
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change in the obi programme according to the new obitools3.apps module
creation
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2016-03-28 15:05:02 +02:00 |
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b926ca3997
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A template for a command
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2016-03-28 15:04:06 +02:00 |
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aacfefad26
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A set of utilitaty function for creating commands
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2016-03-28 15:03:26 +02:00 |
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d44117d625
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obiimport function for testing purposes
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2016-03-23 13:00:02 +01:00 |
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4085904362
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Merge branch 'multiple_avls_bloom'
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2016-03-22 14:14:10 +01:00 |
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383e738ab7
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Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git
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2016-03-18 15:49:53 +01:00 |
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3681cecb4d
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Multiple AVLs with bloom filters (very raw test version)
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2016-03-18 11:06:02 +01:00 |
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21d1b2ed3e
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First implementation of taxonomy reading
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2016-03-11 13:56:38 +01:00 |
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6157633137
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prototype for the obi unix command and the count sub command
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2016-03-08 16:06:00 +01:00 |
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a08def47e6
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It is now impossible to create a view with a name identical to one of an
existing written view
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2016-03-01 13:36:54 +01:00 |
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fc5a12bad7
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Closes #34
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2016-02-29 17:56:55 +01:00 |
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e323d8e702
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Cython classes for nucleotide sequences (outside or in the context of a
view)
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2016-02-29 16:33:30 +01:00 |
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4df313c54a
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Added Obiviews specialized for the handling of nucleotide sequences
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2016-02-25 09:43:27 +01:00 |
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ffc68d448f
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Deleted a forgotten print statement
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2016-02-18 15:15:42 +01:00 |
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a8f03248a8
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Major update : views
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2016-02-18 10:38:51 +01:00 |
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c139367555
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DNA sequences and character strings are now handled using AVL trees.
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2015-12-11 17:24:44 +01:00 |
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1586956d57
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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.
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2015-12-02 17:32:07 +01:00 |
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b45b496b0e
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Major update: new type of columns containing indices referring to lines
in other columns
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2015-11-29 11:57:07 +01:00 |
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2cf10cb6f0
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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')
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2015-11-23 15:48:27 +01:00 |
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5a5516303d
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deleting useless .pyc files
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2015-11-23 14:43:34 +01:00 |
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6aa2f92930
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DNA sequences are now encoded on 4 bits when they are in IUPAC
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2015-11-20 15:32:09 +01:00 |
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6ab1c83302
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New column type for DNA sequences. Only for those coded on 2 bits (only
'ATGCatgc') for now.
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2015-11-19 18:12:48 +01:00 |
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e371248567
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changed version to 0.0.0
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2015-11-19 18:11:21 +01:00 |
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e8417b4f6f
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The endianness of an OBIDMS is now stored in an informations file that
is read when opening the OBIDMS.
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2015-11-16 14:37:51 +01:00 |
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6579566c6e
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Minor changes in code to improve readability and fix C compilation
warnings
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2015-11-10 14:37:58 +01:00 |
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410e2e02a0
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When retrieving the header of a column, the version number of the column
wanted can now be provided.
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2015-11-10 13:30:10 +01:00 |
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661fe3606a
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In OBI_CHAR columns, characters are now given and retrieved as decoded
(unicode) characters.
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2015-11-10 11:24:08 +01:00 |
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c4b7e579cf
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Comments in column headers are now working.
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2015-11-10 10:56:45 +01:00 |
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0e3d6ed2d7
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Methods __len__ (number of lines used) and __sizeof__ (total size in
bytes) implemented for columns.
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2015-11-09 15:56:20 +01:00 |
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9b066f4327
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Major update: obiarrays with columns containing indices referring to
character strings.
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2015-11-06 17:55:15 +01:00 |
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456551ffeb
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obi arrays that don't work because of cython bug passing wrong pointers
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2015-11-03 14:22:00 +01:00 |
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ecb9d97adb
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Reorganized the code to have less functions, and the functions to get
and format the creation date of a column are now working.
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2015-10-15 15:12:45 +02:00 |
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0eaa5aa784
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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
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2015-10-14 18:05:34 +02:00 |
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21923e213d
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The unit tests now test for None values
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2015-10-12 18:02:40 +02:00 |
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dbed3d9d1d
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New module for unit testing with PyUnit
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2015-10-09 15:42:57 +02:00 |
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ebc9f6f512
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fixed a bug where Cython was casting doubles in floats
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2015-10-08 15:28:30 +02:00 |
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2b3f03ec28
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Removed deprecated script
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2015-10-08 10:46:46 +02:00 |
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b553eef781
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Method to close a DMS is uncommented but not complete yet (columns have
to be closed separately)
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2015-10-08 10:44:13 +02:00 |
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392f110c8d
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new functions in the OBIDMS_column class to raise NotImplementedError
exceptions and to get the creation date of a column
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2015-10-02 13:51:26 +02:00 |
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eeebbc77c3
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missing __init__ file in previous commit
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2015-09-28 13:52:13 +02:00 |
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72155c3b73
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entirely reworked cython wrapper
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2015-09-28 13:51:35 +02:00 |
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9aaf2d264a
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test
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2015-09-25 11:29:17 +02:00 |
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0951934f77
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test
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2015-09-25 11:28:23 +02:00 |
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68b6ab3224
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working on the cython wrapper. This doesn't compile
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2015-09-24 11:32:09 +02:00 |
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