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87044b41d8
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modified the encoding function on 2 bits a little
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2015-11-20 11:32:47 +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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dbf9463238
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The endianness of a DMS is now stored in the OBIDMS structure
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2015-11-18 15:35:09 +01:00 |
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eb12af4da4
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Fixed minor error in the documentation of a function.
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2015-11-16 15:38:01 +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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8ce4f264aa
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When enlarging a column, the function doesn't try anymore to keep the
mapped region at the same pointer (never works), and unmap/remap
instead.
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2015-11-10 13:18:36 +01:00 |
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d885eb48ff
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The header size when creating a column is now calculated according to
the size of the header structure and the page size of the platform.
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2015-11-10 13:09:30 +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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f6ec8ba963
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The header size is now directly read in the file when a column or an
array is opened.
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2015-11-09 17:50:32 +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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01bfc14503
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The data size in bytes is now stored in the header of a column.
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2015-11-09 15:55:00 +01:00 |
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65c1b1e8b2
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Minor changes to make the creation of files and directories cleaner
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2015-11-09 15:22:01 +01:00 |
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b37bd8f21c
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File descriptors for dms, column and array directories are now stored in
structures.
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2015-11-09 15:06:02 +01:00 |
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05e3956a0c
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Minor changes in code to improve readability (freeing some character
strings earlier)
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2015-11-09 11:22:51 +01:00 |
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9b066f4327
|
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
|
Reorganized the code to have less functions, and the functions to get
and format the creation date of a column are now working.
|
2015-10-15 15:12:45 +02:00 |
|
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0eaa5aa784
|
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
|
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
|
2015-10-12 18:02:40 +02:00 |
|
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6877fc4892
|
Fixed a critical bug where values were initialized to NA at the wrong
location when there was multiple elements per line
|
2015-10-12 17:54:36 +02:00 |
|
|
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dbed3d9d1d
|
New module for unit testing with PyUnit
|
2015-10-09 15:42:57 +02:00 |
|
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fc8bf16769
|
Fixed a critical bug in the computation of the new number of lines of a
column when truncating
|
2015-10-09 13:49:48 +02:00 |
|
|
|
e114a3c9cb
|
fixed a critical bug where data size was not calculated correctly and
column directory is now closed when column is closed
|
2015-10-09 10:25:40 +02:00 |
|
|
|
ebc9f6f512
|
fixed a bug where Cython was casting doubles in floats
|
2015-10-08 15:28:30 +02:00 |
|
|
|
2b3f03ec28
|
Removed deprecated script
|
2015-10-08 10:46:46 +02:00 |
|
|
|
8fd9c06be2
|
Fixed missing file for documentation compilation
|
2015-10-08 10:45:54 +02:00 |
|
|
|
b553eef781
|
Method to close a DMS is uncommented but not complete yet (columns have
to be closed separately)
|
2015-10-08 10:44:13 +02:00 |
|
|
|
ee4c513fd4
|
Fixed a bug where cloning a column would fail if the data was empty
|
2015-10-08 10:36:02 +02:00 |
|
|
|
c013e6ad33
|
fixed typo in doxygen doc
|
2015-10-08 10:33:19 +02:00 |
|
|
|
c98d567e2f
|
Updated the documentation and restructured a bit because it wasn't
compiling (note: Breathe not working)
|
2015-10-06 11:09:01 +02:00 |
|
|
|
392f110c8d
|
new functions in the OBIDMS_column class to raise NotImplementedError
exceptions and to get the creation date of a column
|
2015-10-02 13:51:26 +02:00 |
|
|
|
6ced3c4896
|
new functions to get the creation date of a column
|
2015-10-02 13:47:53 +02:00 |
|
|
|
4b8bf41a71
|
closes #13, obi_errno is initialized to 0
|
2015-10-02 13:46:34 +02:00 |
|
|
|
c59a244e9d
|
Fixed little typo
|
2015-09-30 12:07:13 +02:00 |
|
|
|
4b7f2d268b
|
Doxygen documentation corrected and completed.
|
2015-09-30 12:03:46 +02:00 |
|
|
|
45af8396b8
|
minor change in variable name for better coherence
|
2015-09-28 13:52:41 +02:00 |
|
|
|
eeebbc77c3
|
missing __init__ file in previous commit
|
2015-09-28 13:52:13 +02:00 |
|
|
|
72155c3b73
|
entirely reworked cython wrapper
|
2015-09-28 13:51:35 +02:00 |
|
|
|
9aaf2d264a
|
test
|
2015-09-25 11:29:17 +02:00 |
|
|
|
0951934f77
|
test
|
2015-09-25 11:28:23 +02:00 |
|
|
|
68b6ab3224
|
working on the cython wrapper. This doesn't compile
|
2015-09-24 11:32:09 +02:00 |
|
|
|
b0570ee486
|
fixed permissions when creating files
|
2015-09-22 15:52:07 +02:00 |
|
|
|
72105b2aed
|
fixed the computation of the data size when cloning a column
|
2015-09-22 10:27:17 +02:00 |
|
|
|
9ab8a42340
|
fixed the mkdir permission mode that forced the user to use sudo to
write in the created directories
|
2015-09-21 15:48:02 +02:00 |
|
|
|
7b606c0477
|
Column files now always have a size that is a multiple of the page size,
and the function that enlarges mapped column files tries mapping on next
byte before unmapping/mapping again
|
2015-09-21 15:42:29 +02:00 |
|
|
|
7d7dbb1bf9
|
Handling of single char columns
|
2015-09-18 15:49:15 +02:00 |
|
