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532d8e9cd7
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obi import: small efficiency improvement when dealing with NA values
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2017-10-04 15:44:48 +02:00 |
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b4088a7928
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Cython API: Added basic taxonomy option
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2017-10-04 15:42:17 +02:00 |
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ae24a807da
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obi uniq: added the option to merge ids, except it only works on small
sets until lists are implemented properly using obiblobs
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2017-09-25 17:28:03 +02:00 |
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75c15594c4
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obi uniq: added option to use categories additionally to the sequence to
determine uniqueness
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2017-09-25 10:56:43 +02:00 |
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41dec03448
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Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git
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2017-09-18 16:08:31 +02:00 |
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a776e46e6d
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Add the command name in the log
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2017-09-15 14:51:13 +02:00 |
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0e140df0fb
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Cython API: added some imports in __init__ files
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2017-09-14 18:30:04 +02:00 |
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73bca6288f
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New obi uniq
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2017-08-20 18:04:21 +02:00 |
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6a2759eee6
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obi import with new input/ouput API
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2017-08-20 17:58:36 +02:00 |
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663a1a1091
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Cython API: column elements: added possibility to check if an element
exists from its index, and a dict-like get() method
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2017-08-20 17:44:05 +02:00 |
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c6d5436a58
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Cython API: fixed a bug where iteration on a NUC_SEQS view would not be
done correctly (bug appeared with optimization modifications done
lately)
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2017-08-20 17:41:41 +02:00 |
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47cad285d6
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Cython API: fixed 2 little bugs in Seq API
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2017-08-20 17:39:30 +02:00 |
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74f15d1a23
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Cython API: Various fixes in input handlers (parsers, openers etc).
Mostly working but not bug-free
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2017-08-20 17:37:51 +02:00 |
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7f1ff49aa2
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Cython API to import a column and a view from a DMS to another DMS
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2017-08-03 16:34:02 +02:00 |
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407f61a408
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Add the possibility to create temporary objects like a temporary
directory and a temporary DMS
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2017-07-28 16:33:19 +02:00 |
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35b0c55a8c
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Cython API: various improvements and checks
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2017-07-28 13:15:13 +02:00 |
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b9c65a871f
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Patch decoding of URL
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2017-07-28 12:41:28 +02:00 |
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84bb93096f
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Cython API: fixes and improvements in Column API
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2017-07-28 10:27:04 +02:00 |
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01c69e7e25
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Cython API: fixed a bug when printing a column
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2017-07-28 10:01:56 +02:00 |
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adf5cbef97
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Added DMS method to create a DMS if it doesn't already exists, otherwise
opens it
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2017-07-28 09:55:43 +02:00 |
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da48a9d1af
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Patch group of option : types must be callable not a string
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2017-07-28 09:36:18 +02:00 |
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9482c663c0
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minor comments and changes
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2017-07-27 19:46:34 +02:00 |
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89e2f80fd8
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Goes with previous commit
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2017-07-27 19:43:00 +02:00 |
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7112f44fb7
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Bug fixes for input handlers, openers, parsers etc. Compiling but not
tested
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2017-07-27 19:42:44 +02:00 |
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b2fc1f4611
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obi uniq: first version
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2017-07-27 19:40:19 +02:00 |
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75f691d55a
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Cython API: Seq classes reworked
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2017-07-27 19:39:58 +02:00 |
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0655063bb0
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Cython API: view_NUC_SEQS changes to go with previous commits
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2017-07-27 19:39:26 +02:00 |
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9701b1230c
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Cython API: OBIWrapper.new method is now OBIWrapper.new_wrapper to avoid
mismatching method definitions with subclasses
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2017-07-27 19:38:25 +02:00 |
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f8a4428674
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Cython API: DMS test_open method doesn't raise an exception anymore
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2017-07-27 19:36:28 +02:00 |
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1a0f18a11a
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Cython API: added a __setitem__ method to the View class that can detect
if the item is a Line and create the corresponding columns if needed +
minor changes
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2017-07-27 19:35:28 +02:00 |
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3d7aa52c90
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Cython API: Fixed a bug when setting NA values in Column_multi_elts, and
added some properties
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2017-07-27 19:31:15 +02:00 |
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69c50ff922
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Cython API: added a Column subclass to allow direct access to indexes
for columns that store indexes referring to other data
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2017-07-27 19:29:10 +02:00 |
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c91969126b
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Cython C API declarations to go with previous commit
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2017-07-27 19:26:59 +02:00 |
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15d383fa8b
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Added possibility to specify the offset for encoding and decoding
sequence quality character strings
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2017-07-27 19:24:41 +02:00 |
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99ceed5fff
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Cython API: renamed OBI_Taxonomy to Taxonomy and OBI_Taxon to Taxon
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2017-07-27 19:21:45 +02:00 |
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fa8f826cdc
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Cleanup the end of the file
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2017-07-27 16:07:39 +02:00 |
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dc91174a5e
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Complete the input option group functions
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2017-07-27 16:06:48 +02:00 |
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ec65f00cf2
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Complete the fasta iterator to manage new input options
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2017-07-27 16:05:30 +02:00 |
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8d9cdb4d03
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Complete the fastq iterator to manage new input options
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2017-07-27 16:05:17 +02:00 |
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949e5f9baf
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Make a first full version of the URI decoder
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2017-07-27 16:04:31 +02:00 |
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3c6a05be54
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Add option to the default config corresponding to the parsing of the
inputs
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2017-07-27 16:03:47 +02:00 |
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8781ecab1f
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Add a factory checking the file format and returning the correct
iterator. First version working only with fasta and fastq nucleic
formats
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2017-07-27 16:02:52 +02:00 |
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0f6ae7dfa6
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Options stuff... ;-)
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2017-07-25 13:07:03 +02:00 |
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28259cd88b
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Beginning of URI decoder -- !!! NOT YET FULLY IMPLEMENTED !!!
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2017-07-25 13:05:58 +02:00 |
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b24be84b0a
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Add a first group of options
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2017-07-25 11:14:30 +02:00 |
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ced9a268a1
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obi import: added an option to specify the NA value in the input file
(default is 'NA', same as in R's read.table function)
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2017-07-11 12:10:33 +02:00 |
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df2ad41150
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Cython APi: Added a width property to views, corresponding to their
column count
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2017-07-11 11:46:32 +02:00 |
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f8895e879d
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Cython API: Added a function to get a column from its index in the view
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2017-07-11 11:36:42 +02:00 |
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b729b8928f
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obi less: fixed bug when the length of a view would be less than the
default number of lines printed
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2017-07-10 17:04:02 +02:00 |
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b6b95f26b6
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obi import: Skipping sequences is now done through the iterators so that
sequences are not uselessly parsed
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2017-07-10 17:02:30 +02:00 |
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