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98d0849653
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Sequence alignment: added the possibility to specify the index of the
sequences to align in a column containing multiple sequences per line (C
level for now)
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2016-11-29 16:15:02 +01:00 |
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76a4c6b14e
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Fixed a bug when cloning a view and checking its type
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2016-11-23 11:28:17 +01:00 |
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70c49e214a
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Added the kmer filter to LCS alignments, and now obiblobs containing
encoded sequences are directly put in int16_t arrays for the alignment
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2016-11-18 16:29:28 +01:00 |
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1c71c195fc
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Goes with a0ebc2d8
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2016-11-10 15:01:29 +01:00 |
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359578814b
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Added view type property to OBIView cython class and updated obi export
to use it
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2016-11-08 17:49:59 +01:00 |
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51b23915ca
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Added properties for Nuc_Seq cython classes (and updated commands using
them)
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2016-11-08 16:59:32 +01:00 |
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b5b889c4a2
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Fixed the OBI_Nuc_Seq_Stored cython class not being up to date with the
new properties of its parent class
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2016-11-08 11:26:37 +01:00 |
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36ac315125
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Fixed bugs with python view type when creating a new view, and a bug
when trying to guess the obi type of a nucleotide sequence when its type
was bytes
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2016-11-08 11:23:54 +01:00 |
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8291693309
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obi grep: updated to work with the new line selection class and within
the local sequence environment, and progress bar functioning
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2016-11-08 11:19:12 +01:00 |
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4bc19c3e49
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obi export: view type is now checked and progress bar functioning
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2016-11-08 11:17:20 +01:00 |
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2d2fe5279d
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Added functions to add new taxa to a taxonomy with handling of
associated *.ldx files
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2016-11-03 17:59:21 +01:00 |
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2504bf0fa9
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Added an iterator to the OBI_Taxonomy cython class
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2016-11-02 11:08:18 +01:00 |
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d8a257e711
|
Taxonomy handling functions in C. Features: read taxdump, read binary
files, write binary files. Not fully handled yet: *.adx, *.pdx, *.ldx,
merged.dmp and delnodes.dmp files.
|
2016-10-27 18:56:11 +02:00 |
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b63d0fb9fb
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Added C functions to write .rdx, .tdx, .ndx binary taxonomy files from a
taxonomy C structure
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2016-10-14 17:03:10 +02:00 |
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1b07109e51
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Removed deprecated code
|
2016-10-10 17:01:51 +02:00 |
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60ab503a14
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Added properties in the OBI_Taxonomy class
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2016-10-10 17:01:17 +02:00 |
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2dcfdc59fc
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When a new view is created with a line selection, the view to clone is
automatically found + compacted redundant code + fixed potential bug
when cloning a NUC_SEQS view by name
|
2016-10-06 17:55:18 +02:00 |
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399fc2c051
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Removed deprecated source files previously used for tests
|
2016-09-30 17:49:37 +02:00 |
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9cd57deca9
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Added OBIView_line_selection class to make new line selections
associated with the view to clone, and improved and renamed method
closing a view
|
2016-09-30 17:48:53 +02:00 |
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d88811ed7d
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Added a seed option to the obi test command for reproducible tests
|
2016-09-29 17:34:48 +02:00 |
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8c402101e4
|
Renamed private attributes as _* and removed some deprecated code
|
2016-09-28 16:56:44 +02:00 |
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b717e8bb8b
|
Added properties for the OBIView class and cleaned up deprecated code
|
2016-09-28 14:26:23 +02:00 |
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03a2c8ef7c
|
Finished restructuring the OBIDMS_column class properties
|
2016-09-27 14:16:30 +02:00 |
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a7f891d1c9
|
Added a lines_used property to the OBIDS_column class
|
2016-09-26 18:04:28 +02:00 |
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bd50b3f972
|
Added version property to OBIDMS_column class
|
2016-09-26 17:45:10 +02:00 |
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81380363b7
|
Added original_name property to OBIDMS_column class
|
2016-09-26 17:31:32 +02:00 |
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a4b8349274
|
Added data_type property to OBIDMS_column class
|
2016-09-26 17:12:20 +02:00 |
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|
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a474391b27
|
Added nb_elements_per_line property to OBIDMS_column class
|
2016-09-26 17:01:13 +02:00 |
|
|
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a0bc45cc92
|
Added elements_names property to OBIDMS_column class
|
2016-09-26 16:53:16 +02:00 |
|
|
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76f89717fe
|
Added alias property to OBIDMS_column cython class
|
2016-09-26 16:12:48 +02:00 |
|
|
|
b408a4f6eb
|
Changed file name limits to adapt to system limits + minor changes
|
2016-09-22 18:05:07 +02:00 |
|
|
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b083745f56
|
Deleted the "new line selection while editing a view" system
|
2016-09-22 11:19:29 +02:00 |
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|
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dd55aef3e5
|
Added column class method to get the unique references (name and
version) of a column
|
2016-09-21 17:08:44 +02:00 |
|
|
|
9ac522fde1
|
Better obi test command
|
2016-09-21 17:06:35 +02:00 |
|
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6adb9eb623
|
Should solde issue #56
|
2016-09-19 21:40:40 +02:00 |
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8f49553d5a
|
First version of the obi test command, testing that the OBITools3 work
correctly
|
2016-09-15 12:26:07 +02:00 |
|
|
|
eb82d088cb
|
Added some view class methods
|
2016-09-05 12:20:00 +02:00 |
|
|
|
8d360b0fac
|
Minor improvements to obi export command
|
2016-08-19 17:49:22 +02:00 |
|
|
|
b34769b27c
|
Minor improvements to obi export command
|
2016-08-19 17:46:55 +02:00 |
|
|
|
2d0a714e37
|
Basic obi export command exporting from view to fasta or fastq format,
for testing purposes
|
2016-08-19 17:40:58 +02:00 |
|
|
|
e4129610cf
|
Quality columns are now optional in NUC_SEQS views + minor fixes
|
2016-08-16 15:17:26 +02:00 |
|
|
|
cf839522e7
|
Minor update and fix to obi grep command
|
2016-08-12 17:45:44 +02:00 |
|
|
|
10b22f79da
|
The cython subclass is now correctly chosen when cloning a view
|
2016-08-12 17:39:19 +02:00 |
|
|
|
ad8e10f2d1
|
Reworked a bit alignment API
|
2016-08-12 15:56:07 +02:00 |
|
|
|
64a745ce0b
|
First very basic version of obi grep command
|
2016-08-11 17:32:08 +02:00 |
|
|
|
d3c58780a0
|
Added __len__ function do OBIViews that returns the line count
|
2016-08-10 17:20:23 +02:00 |
|
|
|
029d395da1
|
Added __iter__ function to OBIView lines
|
2016-08-10 17:08:22 +02:00 |
|
|
|
bea02cc7a5
|
Added (temporary?) check for the type of quality strings because the
import now seems to return them with bytes type
|
2016-08-10 16:25:45 +02:00 |
|
|
|
4ba01617af
|
Fixed obscure compilation bug
|
2016-08-10 15:26:40 +02:00 |
|
|
|
bec684d5e2
|
Fixed merge conflict
|
2016-08-10 15:05:37 +02:00 |
|
