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906343187b
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Fixed bug with view option in obi less and obi check
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2017-07-06 16:42:27 +02:00 |
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c3cd57a9e3
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Removed deprecated file
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2017-07-06 10:57:14 +02:00 |
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101f764cce
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New obi import with rewriting of columns when column type or line
elements (keys) change
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2017-07-05 17:15:23 +02:00 |
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3f5fef10b9
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obi test: minor changes
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2017-07-05 14:37:27 +02:00 |
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20c72af697
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Basic obi check command to check DMS and view informations
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2017-07-05 13:54:19 +02:00 |
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d252131950
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Basic obi less command
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2017-07-05 13:44:12 +02:00 |
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ca16ce0bb0
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Basic obi grep with new Cython API
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2017-07-05 11:58:10 +02:00 |
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4b037ae236
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Updated obi test to test NUC_SEQS views and the taxonomy API
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2017-04-21 12:09:04 +02:00 |
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b998373be5
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Cython API: updated the test command for the new API and deactivated the
other commands for now
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2017-04-14 16:21:33 +02:00 |
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381194194c
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Cython API: compiling but not working
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2017-03-06 16:07:02 +01:00 |
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431c1c8c6a
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Merge branch 'Eric_new_Python_API' of
git@git.metabarcoding.org:obitools/obitools3.git into
Eric_new_Python_API
Conflicts:
python/obitools3/obidms/_obidms.pxd
python/obitools3/obidms/_obidms.pyx
python/obitools3/obidms/_obidmscolumn_bool.pyx
python/obitools3/obidms/_obidmscolumn_str.pyx
python/obitools3/obidms/_obiseq.pxd
python/obitools3/obidms/_obiseq.pyx
python/obitools3/obidms/_obitaxo.pxd
python/obitools3/obidms/_obitaxo.pyx
python/obitools3/obidms/_obiview.pxd
python/obitools3/obidms/_obiview.pyx
python/obitools3/obidms/_obiview_nuc_seq.pxd
python/obitools3/obidms/_obiview_nuc_seq.pyx
python/obitools3/obidms/_obiview_nuc_seq_qual.pxd
python/obitools3/obidms/_obiview_nuc_seq_qual.pyx
python/obitools3/obidms/capi/obialign.pxd
python/obitools3/obidms/capi/obidmscolumn.pxd
python/obitools3/obidms/capi/obitaxonomy.pxd
python/obitools3/obidms/capi/obiview.pxd
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2017-02-20 14:55:36 +01:00 |
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f23315e26f
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New Cython API: compile but doesn't work
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2017-02-17 15:14:06 +01:00 |
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e50da64ea1
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The elements names when a column contains several elements per line are
now formatted with '\0' as separator and handled in a more optimized way
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2017-01-31 16:48:06 +01:00 |
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5c50e5b378
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Embryo of code for openMP parallelization of LCS alignment but
deactivated for now because can't make it compile with cython/clang
|
2016-12-20 11:46:58 +01:00 |
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857a5198e4
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Updated `obi lcs` for the LCS alignment of two columns
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2016-12-16 19:40:36 +01:00 |
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191c83aafc
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Added missing *.cfiles
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2016-12-15 15:28:34 +01:00 |
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8afb1644e9
|
Alignment: API rework. 'obi align' is now 'obi lcs', and the results are
now written to columns automatically created in the output view, all
optimally handled at the C level.
|
2016-12-12 11:58:59 +01:00 |
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fa4e4ffaff
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Changed the cython API to create new views so as to have different
functions for the different cases
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2016-12-07 14:17:57 +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
|
2016-11-18 16:29:28 +01:00 |
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359578814b
|
Added view type property to OBIView cython class and updated obi export
to use it
|
2016-11-08 17:49:59 +01:00 |
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51b23915ca
|
Added properties for Nuc_Seq cython classes (and updated commands using
them)
|
2016-11-08 16:59:32 +01:00 |
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8291693309
|
obi grep: updated to work with the new line selection class and within
the local sequence environment, and progress bar functioning
|
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
|
2016-11-08 11:17:20 +01:00 |
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9cd57deca9
|
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
|
Added a seed option to the obi test command for reproducible tests
|
2016-09-29 17:34:48 +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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a4b8349274
|
Added data_type property to OBIDMS_column class
|
2016-09-26 17:12:20 +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
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Added alias property to OBIDMS_column cython class
|
2016-09-26 16:12:48 +02:00 |
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b408a4f6eb
|
Changed file name limits to adapt to system limits + minor changes
|
2016-09-22 18:05:07 +02:00 |
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9ac522fde1
|
Better obi test command
|
2016-09-21 17:06:35 +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 |
|
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8d360b0fac
|
Minor improvements to obi export command
|
2016-08-19 17:49:22 +02:00 |
|
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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 |
|
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e4129610cf
|
Quality columns are now optional in NUC_SEQS views + minor fixes
|
2016-08-16 15:17:26 +02:00 |
|
|
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cf839522e7
|
Minor update and fix to obi grep command
|
2016-08-12 17:45:44 +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 |
|
|
|
2aaa87edcc
|
1st version of obi align command and reworked functions that handle
column alignment
|
2016-08-10 14:51:02 +02:00 |
|
|
|
3b59043ea8
|
Major update: New column type to store sequence qualities. Closes #41
|
2016-05-20 16:45:22 +02:00 |
|
|
|
d159b921eb
|
Fixed obi import trying to print all lines at the end (source of
segfault?)
|
2016-04-27 13:14:19 +02:00 |
|
|
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a6c8d35491
|
import command a bit modified for tests
|
2016-04-26 14:29:54 +02:00 |
|
|
|
7a88ca619a
|
First obi import (doesn't import tags yet because NA values aren't
handled)
|
2016-04-15 17:00:08 +02:00 |
|
|
|
b926ca3997
|
A template for a command
|
2016-03-28 15:04:06 +02:00 |
|
