|
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e04ea85d1e
|
Fixed problematic __str__ method and useless declarations in the
OBI_Nuc_Seq_Stored class
|
2016-04-15 11:22:05 +02:00 |
|
|
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527d3555f0
|
Moved the functions getting full paths for files and directories to
obidms.c/.h files
|
2016-04-15 11:11:13 +02:00 |
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|
|
71492ad229
|
Made the handling of listing and unlisting opened columns and indexers
functions in the obidms files.
|
2016-04-15 10:49:12 +02:00 |
|
|
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73d64e5aff
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Renamed 'unmap_header' function to 'close_header'
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2016-04-14 15:19:27 +02:00 |
|
|
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4cb52e1632
|
Made the truncating of columns automatic when closing them (note:
already the case for AVLs)
|
2016-04-14 15:13:30 +02:00 |
|
|
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9d042f7bd0
|
Refactored and relocated the set and get functions of all column types,
both within and out of the context of a view
|
2016-04-13 15:10:24 +02:00 |
|
|
|
5ec2d8842e
|
Character string indexer API
|
2016-04-12 17:21:01 +02:00 |
|
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04c9470f7d
|
Fixed and cleaned DNA_seq_indexer API
|
2016-04-12 17:20:24 +02:00 |
|
|
|
be05c889e2
|
DNA_seq_indexer API
|
2016-04-12 16:38:47 +02:00 |
|
|
|
04e3a7b5a9
|
Added more references in cython .cfiles files because it seems necessary
for linux distributions
|
2016-04-12 15:10:54 +02:00 |
|
|
|
d8107533d8
|
Obiblob_indexer API
|
2016-04-12 14:53:33 +02:00 |
|
|
|
cd4e65e190
|
Fixed typo and includes in obiblob files
|
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
|
2016-04-12 11:21:14 +02:00 |
|
|
|
c225cfd8b6
|
Fixed bug with retrieval of values from AVLs (bad cast in byte array
structure)
|
2016-04-11 17:07:22 +02:00 |
|
|
|
966b1325ed
|
Deleted declaration of obsolete public function
|
2016-04-11 11:14:20 +02:00 |
|
|
|
019dfc01b4
|
Branch to refactor and debug (AVLs bugged)
|
2016-04-08 15:38:57 +02:00 |
|
|
|
edc4fd7b3e
|
Fixed minor warning
|
2016-03-25 16:11:52 +01:00 |
|
|
|
ff6c27acf2
|
Implemented the retrieval of values with groups of AVLs
|
2016-03-25 15:35:16 +01:00 |
|
|
|
69856f18dd
|
untested (and no possible retrieval) of CRC used to represent data in
AVL trees
|
2016-03-24 16:38:11 +01:00 |
|
|
|
58ac860cc7
|
Added macro for the bloom filter parameters and deleted old unused
macros for crc
|
2016-03-23 13:33:40 +01:00 |
|
|
|
d44117d625
|
obiimport function for testing purposes
|
2016-03-23 13:00:02 +01:00 |
|
|
|
6bd42132c4
|
Minor fixes to silence warnings and replaced two asprintf uses
|
2016-03-23 12:58:53 +01:00 |
|
|
|
4085904362
|
Merge branch 'multiple_avls_bloom'
|
2016-03-22 14:14:10 +01:00 |
|
|
|
b04b4b5902
|
made POSIX compliant
|
2016-03-21 11:33:06 +01:00 |
|
|
|
383e738ab7
|
Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git
|
2016-03-18 15:49:53 +01:00 |
|
|
|
3681cecb4d
|
Multiple AVLs with bloom filters (very raw test version)
|
2016-03-18 11:06:02 +01:00 |
|
|
|
545ed8111a
|
Code for tests storing data in multiple AVLs.
(note: unretrievable data as implemented)
|
2016-03-11 15:34:55 +01:00 |
|
|
|
86071d30c9
|
Minor improvement in AVL initial size calculation
|
2016-03-11 14:07:40 +01:00 |
|
|
|
21d1b2ed3e
|
First implementation of taxonomy reading
|
2016-03-11 13:56:38 +01:00 |
|
|
|
6157633137
|
prototype for the obi unix command and the count sub command
|
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
|
2016-03-01 13:36:54 +01:00 |
|
|
|
fc5a12bad7
|
Closes #34
|
2016-02-29 17:56:55 +01:00 |
|
|
|
e323d8e702
|
Cython classes for nucleotide sequences (outside or in the context of a
view)
|
2016-02-29 16:33:30 +01:00 |
|
|
|
b350ea0393
|
Fixed minor error
|
2016-02-29 16:28:34 +01:00 |
|
|
|
8e9e21a02e
|
Increased the maximum depth of AVL trees
|
2016-02-29 16:27:23 +01:00 |
|
|
|
4df313c54a
|
Added Obiviews specialized for the handling of nucleotide sequences
|
2016-02-25 09:43:27 +01:00 |
|
|
|
ffc68d448f
|
Deleted a forgotten print statement
|
2016-02-18 15:15:42 +01:00 |
|
|
|
a8f03248a8
|
Major update : views
|
2016-02-18 10:38:51 +01:00 |
|
|
|
cfaf069095
|
Fixed more typos and formatting imperfections.
|
2015-12-11 17:37:25 +01:00 |
|
|
|
a6144eabe2
|
Fixed typos
|
2015-12-11 17:26:20 +01:00 |
|
|
|
c139367555
|
DNA sequences and character strings are now handled using AVL trees.
|
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.
|
2015-12-02 17:32:07 +01:00 |
|
|
|
b45b496b0e
|
Major update: new type of columns containing indices referring to lines
in other columns
|
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')
|
2015-11-23 15:48:27 +01:00 |
|
|
|
5a5516303d
|
deleting useless .pyc files
|
2015-11-23 14:43:34 +01:00 |
|
|
|
d6a99bafea
|
Fixed a major bug with the versioning of columns that was introduced in
f6ec8ba9
|
2015-11-23 13:34:51 +01:00 |
|
|
|
08f2657e18
|
Increased maximum line count of columns to 1^9
|
2015-11-23 13:23:18 +01:00 |
|
|
|
6aa2f92930
|
DNA sequences are now encoded on 4 bits when they are in IUPAC
|
2015-11-20 15:32:09 +01:00 |
|
|
|
87044b41d8
|
modified the encoding function on 2 bits a little
|
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.
|
2015-11-19 18:12:48 +01:00 |
|
