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4ddd1a1c37
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embl iterator: only option on embl directories now works as intended
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2019-02-12 16:46:08 +01:00 |
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08bcbcd357
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ngsfilter: reworked to use apat library
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2019-02-06 18:13:54 +01:00 |
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04a3682307
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Cython API: added API to use apat (pattern search) C library
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2019-02-06 18:12:49 +01:00 |
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8f18907566
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Cython API: changed revcomp attribute of Nuc_Seq class to is_revcomp to
be more explicit
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2019-02-06 18:09:11 +01:00 |
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0b62619e4e
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Various commentaries and insignificant fixes
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2019-01-21 17:32:44 +01:00 |
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c7f5b8d980
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Alignpairedend: added alignment using shifting with best kmer similarity
(low level layer in C and Cython API)
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2019-01-21 17:30:46 +01:00 |
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2a6a112d29
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obi import: fixed writing quality in views when appropriate (but still
not a satisfying solution)
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2018-12-11 19:33:55 +01:00 |
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c437931a35
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Cython: fixed history dot graph for all views, and fixed history
recording for build_ref_db and ecotag
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2018-12-10 17:09:00 +01:00 |
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eb586b2f53
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New command and C functions: obi ecotag
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2018-12-09 19:19:32 +01:00 |
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579f56bb54
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obi align (pouic): fixed bug with the saved config when aligning 2
different views
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2018-12-09 19:15:58 +01:00 |
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6acb21712a
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Missing commit for build_ref_db: C API file for cython
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2018-12-09 19:11:59 +01:00 |
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6f27734d71
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Cython: fxed a bug in INT tuple columns where values were converted to
double instead of int
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2018-11-27 16:14:56 +01:00 |
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ece942e771
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new command: build_ref_db to build a reference database with metadata
for the taxonomic assignment of sequences
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2018-11-27 16:11:18 +01:00 |
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4d51f4f015
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obi import: better checking of whether to import quality
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2018-11-19 11:23:39 +01:00 |
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b0da36cb48
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New command: obi align, except it's called obi pouic for now because of
a Cython compilation bug
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2018-11-07 16:05:48 +01:00 |
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d1f1fd432e
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Minor fixes
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2018-11-07 16:04:17 +01:00 |
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75a28929a7
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Renamed Cython alignment library in an attempt to limit some compilation
bugs potentially involving name conflicts
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2018-11-07 16:03:32 +01:00 |
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8faabd3ebf
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Cython, URI: Fixed a bug when using an output URI with just a view name
to use the default DMS
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2018-11-02 19:04:27 +01:00 |
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35f3e7c30b
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All commands now handle outputing to another DMS + small fixes
|
2018-11-02 19:03:09 +01:00 |
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d09aa43133
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Cython API: added a function to get the full path to the DMS directory
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2018-10-31 14:46:25 +01:00 |
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123e5dc0ac
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Cython URI API: added an argument to only open the DMS and return the
rest as a character string
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2018-10-31 14:45:17 +01:00 |
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320561a582
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Views: Added argument to not automatically create default columns in
typed views, a function to delete a view and fixed view history bug
|
2018-10-31 14:38:05 +01:00 |
|
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d53323e7f4
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Fixed comments bug with obi head and obi tail
|
2018-10-21 17:39:17 +02:00 |
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e18b762d81
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Weird buggy Eclipse commit with nothing changed
|
2018-10-21 17:35:18 +02:00 |
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0a0f0682a9
|
Better handling of errors and exceptions when new view name already
exists
|
2018-10-17 19:47:40 +02:00 |
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4802e32f72
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Cython: Sequence objects: repr() method now returns a Fasta or Fastq
formatted string
|
2018-10-17 16:53:42 +02:00 |
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b027762059
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Cython: export: fixed exception raising when no quality data when
exporting to fastq
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2018-10-17 16:52:51 +02:00 |
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da0e3d4043
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Cython: added full handling of NA strings when importing files
|
2018-10-17 16:41:15 +02:00 |
|
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da76f911db
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Cython: Views: improved repr() method
|
2018-10-17 15:54:03 +02:00 |
|
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61ad2deeca
|
obi uniq: Added line breaks when printing informations to cut progress
bar properly
|
2018-10-17 15:53:28 +02:00 |
|
|
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eb6d5581bd
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Cython: Progress bar: added a cut option to choose whether to do line
breaks every tenth of the full bar, set to False by default for lighter
printing
|
2018-10-17 15:52:26 +02:00 |
|
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343dbc7e4d
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Cython: made the logger lighter (now prints just module name instead of
full module path)
|
2018-10-17 15:49:55 +02:00 |
|
|
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6d018a2d28
|
Cython: Added 'modulename' in the config informations
|
2018-10-17 15:47:44 +02:00 |
|
|
|
df70086384
|
New command: obi export
|
2018-10-17 11:27:50 +02:00 |
|
|
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32d8396ee2
|
Cython: Added fasta and fastq writers
|
2018-10-17 11:27:15 +02:00 |
|
|
|
6a8670d24a
|
Cython: minor fixes
|
2018-10-17 11:26:13 +02:00 |
|
|
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ec73fa840a
|
Cython: obi stats fixed to work with reworked options (forgotten in a
previous commit)
|
2018-10-17 11:25:53 +02:00 |
|
|
|
11032ec90b
|
Cython: Sequence objects: Quality strings are now returned as bytes
instead of str
|
2018-10-17 11:24:44 +02:00 |
|
|
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8a9ba8b0a8
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Cython: Added Column line methods to get a Column line as a str or
bytes, and elements (keys, values) with None values are not returned
anymore
|
2018-10-17 11:23:07 +02:00 |
|
|
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135d3b6e67
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Cython: updated the URI decoding to handle outputs other than DMS
|
2018-10-17 11:21:29 +02:00 |
|
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58589e04be
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Cython: rearranged input and output format options to have both and
updated commands accordingly
|
2018-10-17 11:19:48 +02:00 |
|
|
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e6bbe13d81
|
Cython: fasta and fastq parsers now return bytes and take NA string
argument
|
2018-10-17 11:16:20 +02:00 |
|
|
|
61b00d6013
|
Cython: fastq formatter
|
2018-10-09 16:41:14 +02:00 |
|
|
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8029493c10
|
Cython: fasta and fastq header formatter
|
2018-10-09 16:41:00 +02:00 |
|
|
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aa5ee53478
|
Cython: fasta writer
|
2018-10-09 16:40:30 +02:00 |
|
|
|
e31c8ea57a
|
New command: obi history to print DMS or view history in bash, dot or
ascii formats
|
2018-10-07 19:11:36 +02:00 |
|
|
|
9e700ddc21
|
obi test: updated to test comments
|
2018-10-07 19:10:46 +02:00 |
|
|
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e9a41c5b97
|
Commands: updated for JSON formatted comments with history
|
2018-10-07 19:10:34 +02:00 |
|
|
|
35cf2962cc
|
Cython: DMS: JSON formatted comments and history handling
|
2018-10-07 19:06:59 +02:00 |
|
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74be3c39f0
|
Cython: Views: JSON formatted comments and history handling
|
2018-10-07 19:06:23 +02:00 |
|
