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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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38029b1f77
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Forgot a ;
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2017-08-20 17:56:18 +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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c559ddf487
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BUG FIX: creation of a new column would fail because of a case not
handled when a high number of elements per line would imply less than
one line per memory page
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2017-08-20 17:30:23 +02:00 |
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93cff94e7f
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Fixed some compilation warnings
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2017-08-20 17:25:58 +02:00 |
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9744a48a67
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BUG FIX: seemingly identical obiblobs would have different hash values
because of the padding added by the compiler. Fixed by using calloc
instead of malloc for obiblob memory allocation.
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2017-08-20 17:25:15 +02:00 |
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6afdc9fb5f
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AVLs: Added an error check
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2017-08-20 17:21:06 +02:00 |
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6f202363f4
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Fixed a typo in doc
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2017-08-20 17:20:13 +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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4b86aa67a8
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New C functions to import a column and a view from a DMS to another DMS
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2017-08-03 16:33:12 +02:00 |
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a3e81930c2
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Views: finished handling and documenting the conditions for an existing
column to be added to a view
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2017-08-03 16:32:22 +02:00 |
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644b55b49f
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Fixed doc typo
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2017-08-03 16:29:25 +02:00 |
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927c684fc2
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Utils: new function to copy the content of a file into another file
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2017-08-03 16:28:54 +02:00 |
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344566d9e9
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AVLs: made some functions public and changed some rights to be able to
import AVLs from a DMS to another
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2017-08-03 16:27:43 +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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09ddd74652
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Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git
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2017-07-28 15:57:01 +02:00 |
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7c0d882bc9
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Patch a bug when creating a DMS not in the current directory. Use the
basename function to locate the DMS name instead of the loop...
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2017-07-28 15:56:21 +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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c5f3fdc295
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Increased maximum element names length in columns
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2017-07-27 19:44:49 +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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