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1a2d552567
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Abandoned beginning of functions to apply comparisons to whole columns
(not worth it for now as comparisons are already fast enough)
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2016-05-04 13:39:55 +02:00 |
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bc12360490
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Reworked and commented a bit the cython layer for dms, columns and views
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2016-05-02 15:16:06 +02:00 |
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872071b104
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Removed a list of column pointers kept in the OBIView class that was not
really needed
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2016-05-02 14:23:42 +02:00 |
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baba2d742e
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commenting _obidms.pyx
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2016-04-29 16:07:03 +02:00 |
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0eca86107e
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Pseudo obihead for tests
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2016-04-27 14:27:28 +02:00 |
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0de953a3ef
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pseudo obigrep for tests
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2016-04-27 14:19:55 +02:00 |
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d159b921eb
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Fixed obi import trying to print all lines at the end (source of
segfault?)
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2016-04-27 13:14:19 +02:00 |
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4e4cf46b16
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Added all C files as source files for all cython files to stop having
that kind of problem with linux systems
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2016-04-27 10:44:24 +02:00 |
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6b61533650
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Added more C source files for _obiseq
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2016-04-27 10:41:00 +02:00 |
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419885485b
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Added files in _obitaxo C sources for cython
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2016-04-27 10:30:16 +02:00 |
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a6c8d35491
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import command a bit modified for tests
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2016-04-26 14:29:54 +02:00 |
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366264828e
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Renamed MurmurHash2.c file to murmurhash2.c as it could be a problem
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2016-04-26 14:29:17 +02:00 |
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87935c6678
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Fixed all compilation problems with new function names, locations etc
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2016-04-25 18:35:02 +02:00 |
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92980508c0
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Made the function to clone a column in the context of a view private
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2016-04-25 18:15:25 +02:00 |
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1fbbdd43f9
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Updated obiversion_t declaration
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2016-04-25 17:58:37 +02:00 |
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8cdfbb379e
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Documentation for views and reworked the code a little
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2016-04-25 17:58:12 +02:00 |
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7a88ca619a
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First obi import (doesn't import tags yet because NA values aren't
handled)
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2016-04-15 17:00:08 +02:00 |
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eddd19a245
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Changes in obi commands
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2016-04-15 16:59:21 +02:00 |
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2aafecc3b5
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Changed sequence 'description' to 'definition' everywhere
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2016-04-15 16:31:43 +02:00 |
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094b2371e9
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Deleted obsolete directory
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2016-04-15 14:44:31 +02:00 |
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c1034d300d
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merging and fixed git conflict with obiavl.h
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2016-04-15 13:23:29 +02:00 |
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02d67c257f
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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
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2016-04-15 12:55:26 +02:00 |
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e04ea85d1e
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Fixed problematic __str__ method and useless declarations in the
OBI_Nuc_Seq_Stored class
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2016-04-15 11:22:05 +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
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Made the truncating of columns automatic when closing them (note:
already the case for AVLs)
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2016-04-14 15:13:30 +02:00 |
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9d042f7bd0
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Refactored and relocated the set and get functions of all column types,
both within and out of the context of a view
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2016-04-13 15:10:24 +02:00 |
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5ec2d8842e
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Character string indexer API
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2016-04-12 17:21:01 +02:00 |
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be05c889e2
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DNA_seq_indexer API
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2016-04-12 16:38:47 +02:00 |
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04e3a7b5a9
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Added more references in cython .cfiles files because it seems necessary
for linux distributions
|
2016-04-12 15:10:54 +02:00 |
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d8107533d8
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Obiblob_indexer API
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2016-04-12 14:53:33 +02:00 |
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6fe4c6134a
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Allows for calling getConfiguration without parametter for geting the
default configuration
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2016-04-11 13:31:09 +02:00 |
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019dfc01b4
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Branch to refactor and debug (AVLs bugged)
|
2016-04-08 15:38:57 +02:00 |
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45c9c5075c
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A first version of the fasta parser
|
2016-04-01 18:15:54 +02:00 |
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20b97c972b
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Add boolean type in the tag evaluation
|
2016-04-01 13:42:24 +02:00 |
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efc4a4a3c6
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Reduce the call count to eval. This reduce by 3 the time of fast(q|a)
header processing
|
2016-04-01 08:54:06 +02:00 |
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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
|
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
|
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
|
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
|
2016-03-29 18:21:04 +02:00 |
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2dfab3f378
|
Some changes in relation with the new obitools3.apps module
|
2016-03-28 15:05:59 +02:00 |
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e583098a96
|
change in the obi programme according to the new obitools3.apps module
creation
|
2016-03-28 15:05:02 +02:00 |
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b926ca3997
|
A template for a command
|
2016-03-28 15:04:06 +02:00 |
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aacfefad26
|
A set of utilitaty function for creating commands
|
2016-03-28 15:03:26 +02:00 |
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ff6c27acf2
|
Implemented the retrieval of values with groups of AVLs
|
2016-03-25 15:35:16 +01:00 |
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69856f18dd
|
untested (and no possible retrieval) of CRC used to represent data in
AVL trees
|
2016-03-24 16:38:11 +01:00 |
|
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d44117d625
|
obiimport function for testing purposes
|
2016-03-23 13:00:02 +01:00 |
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4085904362
|
Merge branch 'multiple_avls_bloom'
|
2016-03-22 14:14:10 +01:00 |
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383e738ab7
|
Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git
|
2016-03-18 15:49:53 +01:00 |
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3681cecb4d
|
Multiple AVLs with bloom filters (very raw test version)
|
2016-03-18 11:06:02 +01:00 |
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